You finally find out what APOLLO was trying to protect at the bottom of the reactor core....
Those on Sevastopol not killed by the alien creature were brought here to be hosts for more eggs. The walls are covered with some form or resin and every so often, a person is seen hanging from some of the walls, dead.
You decide to destroy the nest by overloading the core...you just have to make it past facehuggers and a host of new adult creatures running about.
Note: I've heard some mention on how could there be eggs if there'd been no queen. In the original movie, the Alien was in the process of creating an egg using Brett's corpse as some form of catalyst.
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