Otherwise the game is a solid shooter, and they even have you crawl into an armored mech suit a couple times, and man the wicked cannon on the APC you roll around in the game on a couple times too. About the only thing I'd fault the game for is that I was sick to death of crawling through ducts and crawlspaces after the first game and the two expansion packs.
Oh, yeah, and the invisible ninja guys are more badass and annoying in this game. Not only do they look more freaky, but they do more damage, are harder to see, and seem to be able to move as fast as you can with the enhancements you gain after the first level of the game.
You are playing a regular Delta Force soldier in this game, so in the first level you have to be a bit more cautious because you don't have the enhanced reflexes to make things as easy as they were right off the bat in the first game. As far as timing, the game starts a little before the first game would've finished, with the end of the first level being the huge mushroom cloud you saw at the end of the first game. Continuity wise, I have to wonder how the ending of the first game would really fit into the second game. IN the end, between both that and the ending of the second game, everything is very wide open for a third game.
Now, as for the ****ed up ****, it is very spoiler heavy, so only read if you don't care about being spoiled.
Apparently Alma ****s you during the last part of the last level. They actually start that off shortly after you reach the surface of the devastated Auburn (which looks really sweet BTW) with your initial encounter with an Adult Alma. At first it's the hag form you saw at the end of the first game, but after you fight her off, she morphs into something much easier on the eyes and the sexual subtext starts there. In the end, after you do what you were supposed to in order to destroy her, it turns out it didn't work, and she appears again, this time very pregnant. In the end, she approaches you and puts your hand over her belly, apparently showing you that your character is the father.
One hell of a note to end the game on. Nothing else after the credits, unfortunately. :-\
Anyway, thought I'd post a few screenshots I took:

"Hot" Alma's first appearance after her adult form attacks you in the elementary school. After this point you see this version of her more than the more familiar ones from the first game and the expansion packs. As you might guess, there's more to this school than meets the eye.

You don't want to get sent to the principal's office at Wade Elementary...
RAPE!!!!

(as in her raping you)