1: Start a closed space system using one of the corridors. For those who don't know what I mean, think entering the corridor at Point A, going through the exit at Point B and reappearing at Point A.
2: Make my Fortress of Doom into a Checkpoint based area... and set the only Checkpoint at the very start. And make the checkpoint... Fragile. *Smirk* This should disable the Save/Load thing.
3: Institute a mandatory Personnel Headcount at random times, If even ONE soldier/mook/eldritch horror is missing, the entire Fortress goes into a Lockdown state. Countering Aggressive/Stealth type characters.
4: If I truly must have a Key to my quarters located somewhere in my Fortress and not on my person where it belongs, It shall either be made of...
The Soul/s (Read: Soul, or Souls) of the Protagonists loved one/s, making them at least hesitant about using it.
Or, some easily enchanted alloy that upon contact with the door will be enchanted to emit a hideously tortured shriek until the key is turned, at which point the key shall fall silent. This same key will also activate a Scanner that will give the protagonist and his/her party hypersensitive hearing before reaching the door, this buff will last until the key is turned, having the convenient effect of destroying their sense of hearing, giving me an advantage.
5: If Necessary I will make the protagonist acknowledge the consequence of his/her actions, meaning if one of my soldiers/mooks dies due to the Protagonist, I will personally provide counselling and commiserations to the family, I will also deliver the news of the death to them myself, This will hopefully make the Protagonist doubt my morality long enough for me to get back to my quarters. When the Protagonist meets me for the first time I will be reading a list containing the Names and Photographs of each and every soldier/mook under my command that were killed by the Protagonist, saying one name for each step S/he takes in my direction, for example...
"Jenkins. J... Did you know him? I did... He was assigned to the Cafeteria... Two years of service and all he got for his trouble was a Knife in the back."
*Step*
"Smith. S... *Slight forced chuckle* You know, every time she and I met in the corridors, she would always flirt with me... I honestly thought she was just being nice, Until after I read her Journal... She actually said that if it cost her soul to further my ambitions she'd willingly give it a thousand times...
Not the company's ambitions...
Not the army's ambitions...
Mine. And I can't even find her personal effects to send to her Family."
If the protagonist makes it to me without dissolving into a sobbing mass of apologies and guilt, I will do as an earlier poster wrote and just give them a large bag of money saying in a dull monotone:
"So Congratulations, You have managed to murder thousands of my friends, you have managed to commit Genocide at least once... Oh, you didn't know? those animals you thought were "Boss Battles" were actually either the last of their species, or an entirely new Life form altogether... The one that continually healed you? I visited it this morning... It healed me, thinking I wanted to play..."
At this point, i would trail off for a short time, my expression shifting into a small smile as though thinking of happier times.
"The scientists I dispatched to raise it? They informed me It had literally no combat potential. So congratulations, You killed someone who couldn't have fought back if they tried. Anyway, take what you like from the fortress and leave, and never return... I know I won't." Before getting up and walking away accompanied by any of my surviving soldiers/mooks.
*Phew* Sorry for the really long post folks.
EDIT: Fixed a bit of the post.