Games with surprise second acts!

[Danbo Jambo]

The Witcher 2.

A second act which is entirely different depending on your choices, and within that sub-choices too, for me you don't actually get the full story of the game until at least the 2nd playthrough.

Even then I'd say playthrough's 3-4 give you the full picture.

 

[maninahat]

Brutal Legend, turning from a third person slasher into a strategy game.

 

[BrawlMan]

Nier: Automata. I mean, I knew it will have a second act, but there are so many surprises it's ridiculous.

You are right, but getting the true ending was so satisfying. And while we are at it; the Drakgengard series as a whole runs off on this.

Guardian Heroes - Depending on the path you take. Let's just say you will be playing the game more than one time for the story.

 

[CaitSeith]

Bloodborne. You pass half the game fighting werewolves, blood-thirsty crazy people and similar monsters. But at certain point you discover the reason behind this nightmare...

Spoiler

And things go full Lovecraft

 

[McMarbles]

Spoiler: VII

Would be a very convincing final fake-out battle with the fake dark lord, if not for the glaring evidence that the game has a second disc you haven't played yet

This is a much bigger surprise in the 3DS version.

 

[Chimpzy_v1legacy]

To start with, I'll give a big shout out to Chrono Trigger which does a pretty good job of setting up a big bad, and setting up a potential climactic showdown to stop said big bad, only to throw you down a deeper rabbit hole.

Spoiler

By the time you get to Magus Castle you've already traveled through most of the different time periods, collected most of the characters, and have a pretty climactic road up to attacking the castle with it's gauntlet of traps, enemies, mini-bosses, and the final show-down with Magus himself which is epic in it's own right. After a difficult and intense battle it's revealed... oh wait you still have half the game left to go through, there's more to see folks! A whole extra time period to visit, new locations in all the previous time periods to see, an extra character (maybe) and lots of side content and story plot twists to really sucker you in.

Let's not even mention those multiple endings...

Chrono Trigger arguably has a surprise third act

Spoiler

when you fight Lavos for the first time in the Ocean Palace. Seems like it might be the final boss. Nope, unless you're on NG+ or obsessively overleveled, you'll get your ass reamed, Chrono will get vaporized and you still have quite a bit of game ahead of you.