And, just as I have to you, done horrible things to them.
Still, she WAS the Queen of the Crown. Mandell made one hell of a foil in that one, and while she could be horribly cheesy in the series...well, so could you (remember that Simon LeBon impression you did at the Battle of the Bands?). Fanfic in your universe scraps the cheese factor and amps up the things which made you stand out from the crop of cartoons in the 1980's - most of which were fucking brutal.
As to why I let you watch while your teammates were being tortured? Simple - everyone, including you - needed to face their Achilles Heel. Doc had to take a leadership position and face being alone - two things he hates and fears. For the same reason, Goose had to be rendered helpless and Niko had to face the dark seed of ther utopian civilization. These things had to be done. You could not defeat the fanfic rendition of your greatest foe unless you defeated your own nightmares.
As for the sequel? I've failed you there. I'm not sure that any justice can be done to the things you and the others went through, and it may be better to picture a happy, peaceful ending with Eliza.