Route A will have the Security Team heeding the advice of Field Marshal Lee. They decide it is best to destroy the entire colony by overloading the reactor. Doing so will prevent the infestation from spreading any further, but will destroy all Helium-3 mining operations. This path has the team hold out in the Reactor Core, then fleeing Apollo during the Evac sequence with Hephaestus in pursuit.
Route B has the Security Team taking orders from General Koller. They must save Apollo by any means, as its H-3 Mining operations are too vital to Earth's survival to lose. Far longer and more dangerous, this route has the team using the Devastators in their battle with Athena and her massive hordes, as well as engaging in the climatic final battle with Hades.