Mass Effect 2 Plot Holes (Spoilers)

AcacianLeaves

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Yeah, that's right another ME2 thread. Before you start I used the search function and didn't find a similar topic.

Also, obviously, Spoilers.

Anyway, I love the game. I think it has far superior gameplay and the story's focus on characterization and personal moments was a great way to tell the story of ME2. Looking forward and back I'd say it's one of the best games of the last decade. I am a tragic case of ME fanboy.

However I couldn't help but notice a few things that bugged me about the main mission story.

1. The Omega 4 Relay
Most of ME2 is spent discussing the suicide mission that is traveling through the Omega 4 Relay. It is the ONLY way to the source of the Collectors and going through it is almost certain death. However...doesn't this work both ways? If I recall, Mass Relays work like giant two-way teleport systems. So as soon as Cerberus learns that the Omega 4 Relay is the source of the Collectors - why don't they just destroy it? If you destroy the Omega 4 Relay, you cut off the Collectors from the rest of the galaxy and isolate them in their homeworld in the galactic core. As the plot says, they can't just fly away from their homeworld because it is surrounded by a large Mass Effect shield that protects it from the black holes and anomalies. They HAVE to use the Omega 4 Relay to travel ANYWHERE in the galaxy. If you destroy it (or disable it if destroying it would be too dangerous), they're stuck. End of story. We win. Why does no one consider this option? If the idea is to save the humans that were abducted, why is the Paragon decision to blow the Collector base to smithereens without rescuing anyone outside of your crew? Also, if the hidden intention of Cerberus was to utilize Collector and thus Reaper technology, why doesn't anyone on the crew consider this as an option?

2. The Human Reaper
I...don't get it. Why were they doing this? What purpose does this serve the Reapers? There are presumably hundreds, thousands, maybe even millions of Reapers in dark space. While the human Reaper looks badass and made a great end-game boss, it never really made any sense to me. Why are they using organic tissue? Why is that necessary? There wasn't anything organic about Sovereign that I could see. Why does the Reaper take on the image of the race that it conquers? Were all previous races squid-like? Why don't any Reapers look like keepers or Protheans? What did the Collectors plan to do with the human Reaper if it was completed? Stomp around on Earth like Godzilla? Why is it necessary to give it all the weaknesses of a human form - like frail limbs and obvious weak spots? Why is is so small compared to Sovereign? This is more than likely something I missed on my first two play-throughs, but I did not understand the ultimate plot of the Collectors (and thus the Reapers) in Mass Effect 2. Especially since we already saw that one Reaper would be torn to pieces by the united races of the galaxy as in Mass Effect 1.

3. What did we actually accomplish in ME2?
Well...nothing really. This isn't so much a plot hole as it is a plot problem. We stopped the Collectors from making a single additional Reaper that would add ONE to the coming fleet of thousands. We did not stall the actual Reaper fleet in any way, as we did in ME1. We did not expose the threat of the Reapers to the galaxy. We did not defeat any actual Reapers, just a single half-made prototype. We didn't even slow them down, or defeat an agent that was attempting to hasten their arrival. We killed a single Reaper that was not related to the original Reaper threat created in ME1. The game ends with the galaxy in the exact same situation it was in at the beginning. Sure, we learned a few things about Reapers, but we didn't actually do anything to stop or slow their arrival.


Now to reiterate, I loved the game. But I felt because of these plot holes that the story suffered. The character moments were well written and interesting, but the main plot could have used a lot more refinement.

So convince me that these are not actually plot holes/problems, or tell me some plot holes that you may have discovered. As I said I am a Mass Effect fanboy, so I'd really like someone to come in and tell me it's alright and that these plot holes have logical and reasonable explanations to them.
 

Talvrae

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AcacianLeaves said:
2. The Human Reaper
I...don't get it. Why were they doing this? What purpose does this serve the Reapers? There are presumably hundreds, thousands, maybe even millions of Reapers in dark space. While the human Reaper looks badass and made a great end-game boss, it never really made any sense to me. Why are they using organic tissue? Why is that necessary? There wasn't anything organic about Sovereign that I could see. Why does the Reaper take on the image of the race that it conquers? Were all previous races squid-like? Why don't any Reapers look like keepers or Protheans? What did the Collectors plan to do with the human Reaper if it was completed? Stomp around on Earth like Godzilla? Why is it necessary to give it all the weaknesses of a human form - like frail limbs and obvious weak spots? Why is is so small compared to Sovereign? This is more than likely something I missed on my first two play-throughs, but I did not understand the ultimate plot of the Collectors (and thus the Reapers) in Mass Effect 2. Especially since we already saw that one Reaper would be torn to pieces by the united races of the galaxy as in Mass Effect 1.
Probably will be explained in ME3... they did get some thing to think about it if you investigate the question... Like that it might be part of the reproduction process of the Reaper and that Reaper are a mix of organic and non-organic materials
 

Booze Zombie

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The Illusive man wanted the Reaper's tech to fight them with, that tech being contained within their base.

Reapers seemingly are created when you melt down a race of people into one being, meaning that to make more reapers, they need to harvest living beings, so reapers exist to commit genocide to live.
That's how they make more of them, they're a self-perpetuating cycle of death.

Also, the reaper Shepard fought? That was it's baby stage.
It would've ended up looking like some kind of human-ship, perhaps, or maybe evolve into the squid shape.

You stopped humanity from being liquified into reaper metal, "freed" The Collectors from their eternal slavery and got a team of powerful people following you, you stop one situation from escalating and now you have to deal with the real problem, the big one.

Mass Effect 3, here we come.
 

Beatrix

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1. Because this way it's like a nice no-rush bossfight waiting to happen. I agree though, poor choice of design.

2. I completely agree, that was just too far-fetched.

3. We set the stage for Mass Effect 3, of course. EA counts on your continued supply of money to feed their poor starving evil empire.
 

Eagle Est1986

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1. Perhaps the Omega 4 relay on the Collectors side works to multiple relays, better to destroy the Collectors, just to be sure.
Also, the reason you only save your crew is because everyone else is already dead, you only just got to your crew in time (or not as the case may be), and you go after them nearly straight away after they're captured.
2. Well considering that thing was only a fraction of the size of your average Reaper, I'd suggest that that thing is just the middle of a Reaper, an 'embryo' stage if you will.
3. You saved Earth, The Collectors were planning to harvest Earth to help create that Reaper.
 

Silvance

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1. The Omega 4 Relay
Most of ME2 is spent discussing the suicide mission that is traveling through the Omega 4 Relay. It is the ONLY way to the source of the Collectors and going through it is almost certain death. However...doesn't this work both ways? If I recall, Mass Relays work like giant two-way teleport systems. So as soon as Cerberus learns that the Omega 4 Relay is the source of the Collectors - why don't they just destroy it? If you destroy the Omega 4 Relay, you cut off the Collectors from the rest of the galaxy and isolate them in their homeworld in the galactic core. As the plot says, they can't just fly away from their homeworld because it is surrounded by a large Mass Effect shield that protects it from the black holes and anomalies. They HAVE to use the Omega 4 Relay to travel ANYWHERE in the galaxy. If you destroy it (or disable it if destroying it would be too dangerous), they're stuck. End of story. We win. Why does no one consider this option? If the idea is to save the humans that were abducted, why is the Paragon decision to blow the Collector base to smithereens without rescuing anyone outside of your crew? Also, if the hidden intention of Cerberus was to utilize Collector and thus Reaper technology, why doesn't anyone on the crew consider this as an option?
Didn't the Reapers create the mass relays? So if we destroy them, doesn't that just delay the inevitable?

2. The Human Reaper
I...don't get it. Why were they doing this? What purpose does this serve the Reapers? There are presumably hundreds, thousands, maybe even millions of Reapers in dark space. While the human Reaper looks badass and made a great end-game boss, it never really made any sense to me. Why are they using organic tissue? Why is that necessary? There wasn't anything organic about Sovereign that I could see. Why does the Reaper take on the image of the race that it conquers? Were all previous races squid-like? Why don't any Reapers look like keepers or Protheans? What did the Collectors plan to do with the human Reaper if it was completed? Stomp around on Earth like Godzilla? Why is it necessary to give it all the weaknesses of a human form - like frail limbs and obvious weak spots? Why is is so small compared to Sovereign? This is more than likely something I missed on my first two play-throughs, but I did not understand the ultimate plot of the Collectors (and thus the Reapers) in Mass Effect 2. Especially since we already saw that one Reaper would be torn to pieces by the united races of the galaxy as in Mass Effect 1.
Remember, Reapers are organic and synthetic beings, they're created by harvesting the genetic materials of a species. It only makes sense that the Reapers would want to replace Sovereign, so they began work on another Reaper. Also, that Reaper was nowhere near finished, who knows, the human form might have been the core of the ship. Or it might be able to transform or some crap, we won't know until ME3.

3. What did we actually accomplish in ME2?
Well...nothing really. This isn't so much a plot hole as it is a plot problem. We stopped the Collectors from making a single additional Reaper that would add ONE to the coming fleet of thousands. We did not stall the actual Reaper fleet in any way, as we did in ME1. We did not expose the threat of the Reapers to the galaxy. We did not defeat any actual Reapers, just a single half-made prototype. We didn't even slow them down, or defeat an agent that was attempting to hasten their arrival. We killed a single Reaper that was not related to the original Reaper threat created in ME1. The game ends with the galaxy in the exact same situation it was in at the beginning. Sure, we learned a few things about Reapers, but we didn't actually do anything to stop or slow their arrival.
We weakened the Reaper threat considerably by stopping the Collectors. It will take time for them to find a new race to enslave. So that's something.
 

Simili

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How easy would it be to destroy the relay? I know the citadel had advanced repair systems and the like and the relays are built along the same lines. If the idea of the relays is to funnel new races towards an easily harvest-able zenith then they need to be built to last.
 

Bellvedere

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Well considering that the collectors were working with the reapers, I think there was a general interest in what they were up too, wouldn't want to leave a dangerous enemy alive especially since they were allies of the reapers who made the mass relays. And you couldn't just deactivate it with others floating around to re-activate it.

Who knows how hard it is to destroy a Mass Relay anyway. Apparently the Protheans couldn't even cut a meteor in half. Also the Relays have been around for thousands of years so clearly they can stand a bit of wear (unlike said meteor).

If they tried to destroy it or deactivate it they'd probably be attacked by stalker keep ship too. Tough work under fire. And they had no support from anyone else because Sheppard is crazy.

Plus the game told me to do it another way.
 

teebeeohh

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1. I might be wrong but i think mass relays can't be destroyed. The reapers likly didn't wont to rebuild half the network every 50000 years to ensure the next wave of organics would reach the citadel
2. so far we have seen squids, which may make up the bulk of the reapers because those were the race that once created them. Maybe they pick out one or two races every time they kill everyone to make new reapers, forced evolution
3. Well I know have a base full of reaper tech and I will have an army of rachni to fight the reapers when they come
 

OwenWalker

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Mass Relays can't be destroyed. If they could, how did the Mu Relay in the first game survive a star going supernova?
 

Jandau

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AcacianLeaves said:
1. The Omega 4 Relay
Most of ME2 is spent discussing the suicide mission that is traveling through the Omega 4 Relay. It is the ONLY way to the source of the Collectors and going through it is almost certain death. However...doesn't this work both ways? If I recall, Mass Relays work like giant two-way teleport systems. So as soon as Cerberus learns that the Omega 4 Relay is the source of the Collectors - why don't they just destroy it? If you destroy the Omega 4 Relay, you cut off the Collectors from the rest of the galaxy and isolate them in their homeworld in the galactic core. As the plot says, they can't just fly away from their homeworld because it is surrounded by a large Mass Effect shield that protects it from the black holes and anomalies. They HAVE to use the Omega 4 Relay to travel ANYWHERE in the galaxy. If you destroy it (or disable it if destroying it would be too dangerous), they're stuck. End of story. We win. Why does no one consider this option? If the idea is to save the humans that were abducted, why is the Paragon decision to blow the Collector base to smithereens without rescuing anyone outside of your crew? Also, if the hidden intention of Cerberus was to utilize Collector and thus Reaper technology, why doesn't anyone on the crew consider this as an option?
I'm not sure the Mass Relays CAN be destroyed. If they can, it might require more firepower than Cerberus can bring to bear. And finally, it's likely that the Illusive Man was planning on capturing the Collector Base from the start or at the very least acquiring their technology to fight the Reapers, which he wouldn't be able to do if the Relay is destroyed.

As for the humans that were abducted, IT IS STATED THAT NONE OF THE COLONISTS SURVIVED. Sorry for the caps, but when you rescue your crew, you also learn that all the other captives were liquified already.

2. The Human Reaper
I...don't get it. Why were they doing this? What purpose does this serve the Reapers? There are presumably hundreds, thousands, maybe even millions of Reapers in dark space. While the human Reaper looks badass and made a great end-game boss, it never really made any sense to me. Why are they using organic tissue? Why is that necessary? There wasn't anything organic about Sovereign that I could see. Why does the Reaper take on the image of the race that it conquers? Were all previous races squid-like? Why don't any Reapers look like keepers or Protheans? What did the Collectors plan to do with the human Reaper if it was completed? Stomp around on Earth like Godzilla? Why is it necessary to give it all the weaknesses of a human form - like frail limbs and obvious weak spots? Why is is so small compared to Sovereign? This is more than likely something I missed on my first two play-throughs, but I did not understand the ultimate plot of the Collectors (and thus the Reapers) in Mass Effect 2. Especially since we already saw that one Reaper would be torn to pieces by the united races of the galaxy as in Mass Effect 1.
This has indeed been poorly explained so far. There are some theories as to why they do it. However, there are a FEW things that can be safely assumed.

Considering its small size (compared to other Reapers) and shape (Reapers are mostly uniform, as you noted), it is possible that the "Human" form will be the CORE of the grown-up version and will be encased in the familiar Space Squid shell later in its development. Since it's basically a Reaper fetus, that would account for all its weaknesses.

As to the "Why" of the matter, that much is fairly obvious if you payed Mass Effect 1. Reapers are stuck in Dark Space (between galaxies) and their original plan relied on opening the Citadel Mass Relay, which is why Sovereign was left behind. It can also be concluded that it requires a fully functional Reaper to activate the Citadel, but Sovreign failed. With Sovreign dead, they need a new Reaper to open the way. To that end, they tasked their agents, the Collectors with "growing" a new Reaper. They picked Humans as their race of choice and got to work kidnapping populations and growing the new Reaper.

3. What did we actually accomplish in ME2?
Well...nothing really. This isn't so much a plot hole as it is a plot problem. We stopped the Collectors from making a single additional Reaper that would add ONE to the coming fleet of thousands. We did not stall the actual Reaper fleet in any way, as we did in ME1. We did not expose the threat of the Reapers to the galaxy. We did not defeat any actual Reapers, just a single half-made prototype. We didn't even slow them down, or defeat an agent that was attempting to hasten their arrival. We killed a single Reaper that was not related to the original Reaper threat created in ME1. The game ends with the galaxy in the exact same situation it was in at the beginning. Sure, we learned a few things about Reapers, but we didn't actually do anything to stop or slow their arrival.
Well, in truth we did the exact same thing that we did in ME1. See my response to #2. We stopped the Reapers' backup plan for opening the Citadel Relay and entering our Galaxy. Granted, this is easy to miss if you miss the point of growing a new Reaper.

I will admit that all this could have been better explained in the game, but I belive I've covered the "plot holes" you mentioned.

If you want a plot hole, try this one: Why the hell did Wilson try to kill you at the start of the game?
 

Gethsemani_v1legacy

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1. The Collectors are not a problem. That's what everyone in the Council is telling themselves, just becaue a Pro-Human Terrorist Group shows up with Commander Shepard (who might have saved the Citadel from a "Geth attack" but is still considered crazy due to all that talk about the Reapers) and says the Collectors are now working with the Reapers that doesn't mean anyone is going to believe them. The Reapers have been dismissed as the delusions of Commander Shepard and why bother with a few stupid human colonists in the Terminus systems that are infamous for being dangerous to begin with with abductions being so common it is almost a daily occurance?

Nevermind such thing as the fact that no one can construct Mass Relays. Dismantling or destroying one means removing it for good. What if someone decides that they one day needs to map the Omega 4 relay? Kind of sucks if you removed it, right?

2. it is established in ME1 aswell as ME2 that the Reapers are cyborgs for a lack of better word. They have both biological and mechanical components. As for the reason they are building a "human" Reaper, it is anyones guess. Some of the more popular theories is that the squid/tick shell of Sovereign and Harbinger is infact an outer carapace (considering the size diffrence between them and the "human") and that they might have a diffrent interior. They might also be building a new Reaper to replace Sovereign to make another attempt at opening the Citadel Relay to let the Reapers out of Dark Space. This would be faster than travelling all the way back to the milky way like they currently seem to be doing.
It should also be noted the Sovereign was only destroyed once it lost its' shield due to Shepards interference. Admiral Hackett/Joker even comments that they can't hurt Sovereign while it retains its' shields.

3. You probably did stall the reaper fleet. Chances were that the "human" reaper would have gone straight to citadel and have torn it all up. Not only that, you also annihilated a race of slaves to the Reapers and disrupted their operation to create more reapers. So in the end, yes the galaxy is pretty much how it was before Shepard bought the farm the first time. But had Shepard not done anything, it would have become a lot worse once the Human Reaper was complete. As it is, denying the Reapers the use of the Citadel is a serious blow to their plans and keeping them from getting a new Reaper into the Milky Way goes a long way to keep them away from the Citadel.
 

Simili

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"If you want a plot hole, try this one: Why the hell did Wilson try to kill you at the start of the game?"

good point. when Miranda shot him I was hoping someone would shout: WILSON! ala castaway.
 

Illanair

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1: You make a valid point as to why they didn't just blow it the shit up. I suppose they realise how dangerous it could be NOT knowing what lies on the other side, and possibly they cling on to the hope that they can bring the kidnapped colonists back - something that would be impossible by blowing it up. Also keep in mind that only Cerberus knows the "truth" about the collectors. If the Council would gain knowledge of this they would probably blow it to smithereens, not knowing better.

2: Why a human reaper? Why a squid reaper in the first game? The human reaper required organic material from humans. Perhaps a Reaper is part organic but won't admit to it, or organic material is just the best renewable source of energy. - who can say if Sovereign isn't composed of some squidlike species (There was that one magazine on Omega with a squid on the cover), and that each Reaper has a unique design, from each species they have consumed over the endless cycles of life.

3: Good point. Not much was actually accomplished in the second game. But the same could be said for alot of other trilogies, with the second movie being "inbetweens". Shephard managed to improve relationships with the Geth and Rachi - perhaps this will be seen as the "gather allies" phase of the trilogy when ME3 hits?

@Simili: The Citadel has a legion of Keepers to mend it. As Anderson mentioned, the repairs are ongoing and won't be finished for another 5 years. A relay could probably be destroyed, but doing it carelessly and with explosives could probably wipe out an entire sector - there aren't kindergarden energy cores.
 

dududf

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Jandau said:
Why the hell did Wilson try to kill you at the start of the game?
Just guess work, but in one of the audios at the begining of the game you can hear Wilson malcontent, and worry about cerberus. i.e. where the hell the funds were coming from. As such he probably thought he was on the moral high ground by trying to destroy the Cerberus base, and thus destroy Sheapard.

AS to why to kill shepard, maybe he didn't know what Cerberus planned to do with him. Maybe he thought they were trying to bring him back and convert him onto Cerberus' sides and use his abilities.

That's a motive right there I believe.
 

richasr

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I agree with the first point, the Omega 4 Relay, but they could have altered the story, have the reapers pouring trough the relay and engaging in this huge battle while you're task is to try and destroy the damn thing before mroe and more get through. I don't really care though.

Human reaper, I imagine more will be explained in the third game, probably will end up explaining more about the Protheans aswell.

You go into the collector base and blow the shit out of a lot of things, including that human reaper, and you also destroy the harbinger's ship, assuming that means the reapers don't have the colelctors - or not as many of tghem at least - to go stealing humans and other such nonsense.
 

Jaranja

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AcacianLeaves said:
1. The Omega 4 Relay
Most of ME2 is spent discussing the suicide mission that is traveling through the Omega 4 Relay. It is the ONLY way to the source of the Collectors and going through it is almost certain death. However...doesn't this work both ways? If I recall, Mass Relays work like giant two-way teleport systems. So as soon as Cerberus learns that the Omega 4 Relay is the source of the Collectors - why don't they just destroy it? If you destroy the Omega 4 Relay, you cut off the Collectors from the rest of the galaxy and isolate them in their homeworld in the galactic core. As the plot says, they can't just fly away from their homeworld because it is surrounded by a large Mass Effect shield that protects it from the black holes and anomalies. They HAVE to use the Omega 4 Relay to travel ANYWHERE in the galaxy. If you destroy it (or disable it if destroying it would be too dangerous), they're stuck. End of story. We win. Why does no one consider this option? If the idea is to save the humans that were abducted, why is the Paragon decision to blow the Collector base to smithereens without rescuing anyone outside of your crew? Also, if the hidden intention of Cerberus was to utilize Collector and thus Reaper technology, why doesn't anyone on the crew consider this as an option?
The relays don't warp you to other relays, they warp you to a place in a different nebula.

AcacianLeaves said:
3. What did we actually accomplish in ME2?
Well...nothing really. This isn't so much a plot hole as it is a plot problem. We stopped the Collectors from making a single additional Reaper that would add ONE to the coming fleet of thousands. We did not stall the actual Reaper fleet in any way, as we did in ME1. We did not expose the threat of the Reapers to the galaxy. We did not defeat any actual Reapers, just a single half-made prototype. We didn't even slow them down, or defeat an agent that was attempting to hasten their arrival. We killed a single Reaper that was not related to the original Reaper threat created in ME1. The game ends with the galaxy in the exact same situation it was in at the beginning. Sure, we learned a few things about Reapers, but we didn't actually do anything to stop or slow their arrival.
The collectors were wiping humans off entire planets and we stopped them, is that not good enough for you?
 

SomeBritishDude

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AcacianLeaves said:
2. The Human Reaper
I...don't get it. Why were they doing this? What purpose does this serve the Reapers? There are presumably hundreds, thousands, maybe even millions of Reapers in dark space. While the human Reaper looks badass and made a great end-game boss, it never really made any sense to me. Why are they using organic tissue? Why is that necessary? There wasn't anything organic about Sovereign that I could see. Why does the Reaper take on the image of the race that it conquers? Were all previous races squid-like? Why don't any Reapers look like keepers or Protheans? What did the Collectors plan to do with the human Reaper if it was completed? Stomp around on Earth like Godzilla? Why is it necessary to give it all the weaknesses of a human form - like frail limbs and obvious weak spots? Why is is so small compared to Sovereign? This is more than likely something I missed on my first two play-throughs, but I did not understand the ultimate plot of the Collectors (and thus the Reapers) in Mass Effect 2. Especially since we already saw that one Reaper would be torn to pieces by the united races of the galaxy as in Mass Effect 1...
I can at least partially answer this one.

The Reapers were created by a race of Squid like creature. These where lightly the precursors to the Protheans. This is why Reapers look the way they do. This is hardly something new. Geth look a lot like the Quarians when they're wearing their hazard suits (I have no idea about under neath) and even in the real world Scientist struggle for robots that look and replicate humans. Also note that we've only met one a few Reapers. There are apparently hundreds in dark space. Many of them may look different, suggesting different designers.

My guess is that each time a civilization fell the Reapers took them over and instructed them to build a Reaper from their own bodys until all of them where dead. This would bring something new to the fleet that gives them an advantage, like how the Asari mate with other species to strengthen their own DNA.The Reapers don't look like the Protheans because the Protheans couldn't create their own Reaper. EDI speculated as much when asked. Maybe the Protheans just aren't compatible with Reaper technology. Maybe the original Prothean reaper didn't survive.

So, after the Prothean Reaper failed the Reapers tried to find a species that would be a good target. They chose humans. There could be many reasons for this. Mordin often spoke of how Humans were one of the most diverse races in the galaxy. This was also pointed out my several other races too. The reprosecutions of this is that Humans are often used as test subjects, as shown once again in Mordins mission. This may be why they are compatible with Reapers. There is also point that Soveriegn was stopped mainly by one human Specter and the Alliance fleet. Maybe the Reapers see humans as the strongest race.

There may not be any organic parts on the reapers that you see but that doesn't mean they don't exist. Metal is more stable than Flesh. Though I will point out that when I went to get the IFF drive the inside of that reaper looked most definitely organic, at least in parts.

Why the Reapers take on the shape of those they conquered may just be a program. Remember the Reapers are machines. Maybe because they where originally created to look like their masters take on the look of other races seemed logical. Or maybe,[b/] just maybe[/b] Bioware wanted you to fight a giant human looking robot. It also gives them license to come up with cool looking Reapers in the final game.

They don't look like the Keepers because the Keepers were created BY the Reapers. There is speculation otherwise I guess. Maybe we'll see a Keeper Reaper (hey that rhymes!) in the final game.

It may be smaller than Soveriegn because the Reapers original creators where bigger than humans.

Maybe it has obvious weak spots because the Reapers are dumb or because the Protheans hadn't finished making it or because bosses with a weakness are classic.

Honestly I know a lot of this was speculation but so was EDIs explanation. It may be explained better in the final game. Obviously if the Reapers only come in the squid like variety it either means Bioware really didn't think it though, the Reapers have only conquered two races, the Protheans and their creators. It also means we could miss out on some badass looking giant robots.
 

Ak1hiro

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The Omega 4 Relay: Remember, the relays are NOT teleportation devices, teleportation does not exist in the Mass Effect Universe. You need only one relay to travel. What the relay does is launch you at a fast enough speed such that travel to other start systems is practical and feasible. The reason that there are always two relays is that you may have to come back to your previous location, so it would make sense to have relays set up in sets. So destroying the relay would only prevent a possible counter-attack against the collectors, they can still show up using their relay from inside. Plus the collectors work for the reapers, they might have the technology to travel w/o the relays, that we do not know of, we will have to wait and see.

As for why is destroying the facility a paragon decision: The base liquefies humans to make a reaper, this is pretty evil.... Imagine Cerberus using this on other species, would you trust Cerberus with this kind of technology? Should technology that causes so much pain, suffering, and outright death(afterwards) be allowed to exist? Oh and remember, the colonists are pretty much dead... remember when you came in some pods were already open.

Human Reaper: Easy, Current reapers looks like (insert 1st species to succumb to reapers here ), since they most likely used (that previously mentioned species) as the organic component. This one uses humans since they are what's available, plus the human one (completed, not in larvae form) would be stronger since it could grab ships). And yes, you do need an organic component, remember how Sovereign linked to the minds of others to control them eventually, that just might require a very large organic component, or the fast repair rate, or the incredibly high intelligence, etc....

What we accomplished: Alot actually, the humans were under attack from the collectors who are aiding the reapers. We stopped the collectors at the end game. We need more allies to fight the reapers, throughout the game, MANY opportunities arise allowing you to form new bonds and unite against the reaper threat, i.e: the geth in the end, the migrant fleet focusing on the reapers instead, etc.... Remember, knowledge is power, and to take down the reapers you will need alot of it. The stage is now set for Mass Effect 3

Hope this helps:)