This is the long version of how I handle the level 12 boss. It starts before I have ever entered the red room, so it shows handling of the minions as well.

The first order of business is to clear the two large rooms close to the entrance. I do this conventionally but cautiously. Next, from outside the boss's lair, I use some of my large collection of guided missiles to take out the two green homer-firing hulks in the far-end side rooms. There is one cool sequence here, where I am surprised by an energy sucker that sneaks through the open door. I manage to gun him down with my Gauss while maintaining control of my guided missile, which goes on to score a direct hit.

With most of the minions gone, I can then grab the cloak in the hidden recharge center and use that to soften up the boss with a few Megas, before putting him away with my final barrage. (See also L12Boss, the short version.)

This grand finale consists of grabbing the invulnerability sphere from the guide-bot cage, tracking down the boss, and unloading my most powerful matter weapons on him. :-) He begins his death dance just as the inulnerability wears off.