Frag rockets don't seem to hurt the shielded hacker.
It's possible to kill the cannon-core, which seems to bug out: If you do it during the scripted fight, the script gets stuck and your ally vibrates.
It is possible to return to the start after some final script elements play. The children are still there, when they're supposed to be somewhere else.
There is one room (I've forgotten exactly where, now) where the door going down is wider than the door going up. I got stuck in the wall in the lower room and had to reset.
I've played it a few times now. My favorite combo is rockets, autosurgeon, cloak+speed.
I've found 18 kids. I've not killed anyone I don't have to - Duke is apparently the only required death, at the end of the first area.
There is a "high-security" zone at the bottom right of Purple. It is unlocked by a panel near the cannon-core, which appears only accessible if you pick a side.
There is also a green area with some plot secrets, which I found accessible after getting the third keycard but before going through the blue area.
With just about everything collected, I have enough to turn on extra ammo and cast-from-HP, and reach the "pacifist" final boss, the forcefield. Does Duke's death count against me? Defeating the forcefield and escaping the room to reach escape shuttle #2 doesn't seem to give me what I'm expecting as the most satisfying ending. Someone help me with what I'm missing.