Nihilanth is dead once and for all! He was enemy #1 in HL, and he would still be an enemy if he were reborn in HL2, which isn't going to happen (I think VALVe would release that would be too cliche). No other aliens team up with you, the Grunts weren't being controlled, they were voluntarily helping Nihilanth. As for the other Xen lifeforms (except controllers), they weren't even helping Nihilanth, they were just creatures that lived on Xen. Here's a list of enemies that were consious of the invasion and helped Nihilanth out:
-Nihilanth (duh) -Controllers -Grunts -Those flying things that warped in Grunts -Vortigaunts (not really helping, but under the control of Nihilanth)
About the Xen Slaves, Nihilanth died so their collars were disabled. The Xen Slaves (Vortigaunts) were never bad, they were under the control of Nihilanth. In HL2, they team up with humans to get revenge.
BTW: If you look carefully at the HL2 trailer in Eli's lab, the Vortigaunt isn't wearing a collar.
The story is that Xen Aliens decided to invade Mars too, and they attack one of the colonies on Mars. You're just a normal guy that lives there and you have to escape.
BTW: This is 50 years in the future, when some of the humans from Earth fled to Mars and built colonies on it.
I'm making a mini-mod/map pack for HL called "Mars Base" which is a working title, not final. There's a small example of my work in the map vault. Go check it out!
BTW: I need some suggestions for the name, that is the purpose of this thread. :
I don't know about the SDK, but while I was searching for it I found the Duct Tape mod for Doom 3. Puts a flashlight at the end of the shotgun and Rifle (or machine gun). Most ppl say it ruins the game, but I don't think so 'cus my moniter is really dark and I'm always dying in the darker areas.
I don't know 'bout a SDK, but if you want Doom3Radiant, open the console and type 'editor'.
It actually uses DOOMedit, or something along the lines of it.