Problem: we've re-created a T-Rex, but it lacks the will to live. Solution: put a wheel of awesome in the room. It will get hats and party, which will fuel its desire to live, despite the fact that it's getting far more spikeballs, wind, and laser than hats and party.
The commander is nigh unto impossible to defeat. He always seems to have a shield, even if you have a shield he can still kill you in about 4 seconds, he enjoys teleporting on top of you with the acid hound, and even if you do a bit of damage he just teleports away and gets health.
Thanks!