Alot of people have trouble with this, but i didn't find it THAT hard. First look for the rocket launcher and get a alot of ammo. Then go to the middle where the invincibility spawns. Get that then follow the arrow next to your guy to the alein. Shoot with rockets until dead, you may need to repeat this process
The invincibility + rocket + 2x damage = pwnage, 3 should definitely kill the alien commander.
Yeah, that's basically what I ended up doing.
But a huge problem I had with that level is dodging the laser beam. It's pretty hard jumping around like a monkey and trying shoot straight with a rocket launcher.