There are other dead scientists with supplies and health packs that you can grab on your way up. After killing the xen masters, make your way to the top of the pit by jumping from platform to platform. Xen masters will assault you when you land. The first room will find you falling down a long narrow pit. So if you need to restock, this is a good place to end up. There is one good advantage to being ported though, The rooms have ample amount of supplies. If this orb hits you, you will be ported into one of 3 rooms where you will be forced to fight off various creatures and head to the port to take you back to Nihilanth's lair. Nihilanth will shoot a green orb periodically. This pool is risky to use, given that Nihilanth has a clear shot to you when he floats up. There is also a platform with a trampoline and health pool. To slow your falls down, try to slide down the walls. But be careful as some of the trampolines will shoot you quite high and could end with you falling to your death. They are needed to get up high enough to shoot at Nihilanth's brain and to reach the crystals. The gravity is drastically reduced here so jumping is quite high. However, like in previous levels, this platform will give way and you will fall down. You will meet Nihilanth face to face on a rock. This will leave his brain exposed to any of your weapons.

There are three external power sources (yellow crystals on the wall) that must be destroyed before Nihilanth's head will periodically open up.

Teleports you to another room where you will have to fight other creatures and make your way to a portal to get back into Nihalinth's lair.

They do some serious damage so be ready to dodge. Nihilanth has two attacks that will deal a lot of damage:

Half life opposing force final boss