All alien activity has ceased for months, but things are far from normal: Norton has logged very peculiar, repeating weather characteristics in their region, of a type never seen before. Meanwhile, Blackwood is being kidnapped by aliens, but at the very last second he Is saved by John Kincaid, an ex-soldier who was drummed out of Ironhorse's unit years earlier by the colonel.
Kincaid performs special jobs for General Wilson, as did his brother Max, until the brother was recently killed by the aliens. While Blackwood tries to decide if Kincaid should be trusted, newly arrived aliens are destroying the old Advocacy for their failures.
At Blackwood's headquarters, Ironhorse learns that General Wilson disappeared several weeks earlier, and the group is now on their own. Wanting to find out what the aliens are up to, Ironhorse leads a reconnaissance mission into the aliens new headquarters. He is captured and his men are killed.
The colonel is cloned by an alien process, and his alien duplicate is instructed to destroy the Blackwood Project records and members. While he is being briefed, Kincaid and Blackwood have entered the headquarters, and find the real Ironside. They manage to escape from the building, but by that time the alien Ironhorse has entered the Blackwood headquarters, and as Harrison calls to warn Norton, the clone kills him and sets explosives to blow up the building.
Just before he dies, Norton sets off the security system, and Suzanne escapes just as Kincaid, Blackwood and the real Ironhorse arrive. They find themselves amid a firefight between Ironhorse's real soldiers and several fake alien ones, but the aliens are soon destroyed. The fake Ironhorse finds Debi, takes her hostage, and forces Blackwood and Kincaid to drop their weapons just as the real Ironhorse, nearly dead from his ordeal, arrives.
Realising the only way to stop the alien clone, and save Debi, is to kill himself, Ironhorse commits suicide. Just after the survivors escape, the headquarters explodes, destroying all their previous research against the aliens. The four remaining Blackwood Project members are now on their own against the threat of the Morthern aliens.