OK, well, I'm not going to explain it fully, because just the thought of it makes my head hurt (
see for yourself).
The beams are all sprites that have their start entitys set to the Nihilanth, and the homing tele beams have their end entitys set on the player. In fact, theres literally over 100 env_beams all over the map that make up all the different effects, so I won't go into that. Here are the main ones:
Also on that pic are alot of the env_ entitys such as the fade in/out and the shake when the fight is over, and most of the sounds triggered throughout the map.
The crystals are set up with sprites, lights, and some other effects and are func_breakables that trigger a bunch of multi_managers so that once all the crystals are broken, the Nihilanth becomes killable.
Those are the trigger_teleports and relays that are used when the Nihilanth hits you with the tele beam.
The rechargers are trigger_hurts that have their values set in the negatives.
Thats the platform you start the map on. The top layer is an autosave, the bottom is the breakable platform,and the outer ring triggers the break.
So, you start on the plat, it breaks, an env_sound of Nihilanth speaking is triggered, he begins to attack using the aformentioned env_beams and sprites, you destroy the crystals which makes Nihilanth succeptable to damage, and then shoot him until his head opens. Then, using the jumppads, which are multi_managers triggering all the sounds and other things that push you in the air, you shoot the boss's head, which is a hit box specified in the actual model. After he dies, a bunch of sprites, beams, sounds, etc. are triggered, and then a changelevel is triggered.
Note that this is a very basic explanation that leaves alot of things out. Maybe I'll submit a tut explaining it more fully.