The final pieces of the plan fall into place as Wraith comes face to face with the Alliance's last ditch effort to save the Earth from the Shadoen Multitude.

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Logan is imprisoned and receives a visit from Sh'lainn. She proposes to perform a mental link, allowing Nick to to uncover his past memories, but Rinaker intervenes and sends Logan to a special confinement on Bikini Atoll. As we finally discover what really happened to Walter Logan, the true enemy is also revealled.

The Shadoen finally reveal their intentions to the world, with a demonstration of their destructive capacities. Now it's up to the new Alliance to take a stand against the upcoming invasion, however can the alien races really put their differences aside and work together for the common good? Meanwhile, Nick and the gang follow clues to find the last contribution of Trueblood to their cause, but a Shadoen attack is underway.

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An Alliance court-martial looks into Nick's handling of a containment and cover-up operation in Seattle. A Tribune alien craft had crashed in the city, and the occupant tried to get a disc to a world-renowned reporter. But as the Alliance tried to convince the world that the craft was a new high-tech weapon employed by terrorists, Nick probed further into the Alliance's webs of deceit, questioning the motives of an organization that would use lethal force against non-hostile aliens.

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The bystander from Nick’s first alien encounter reveals himself as an ex-Alliance operative, joining with Logan, Sh’lainn and the Conduit to take out Rinaker and find the truth about Logan’s father. Rinaker refuses to give up any information on Logan’s father or Omega, and as the former bystander sets the nuclear core to detonate, Logan realizes that his unexpected ally has become becomes an unexpected enemy.

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Sh'lainn predicts that everyone in the Bunker will die in less than twelve hours, but Rinaker ignores the Banshee's fears and proceeds to bring in an alien probe that had been recovered earlier. After touching the alien probe, Sh'lainn is infected by the Iron Death, her Banshee body poisoned from being surrounded by technology. Reduced to the most primal instincts, Sh'lainn tries to destroy the technology that is slowly killing her. But as she tries to detonate the nuclear core that powers the Bunker, Nick rushes to Ireland to find a cure. With a potential explosion radius that would wipe out half of New Mexico, time is running out for the Alliance.

After a STAR assault takes out a combination Lycanthrope weapons dump / hospital, Logan is entrusted with a Lycanthrope cub, Athos, whose mother was killed in the attack. However, Rinaker locks up the child for Alliance study. With Athos' real father, Ruk, launching an attack on Alliance HQ, Logan may have to sacrifice his adopted son to the Lycanthrope pack leader.

Rinaker dispatches Nick and Ti-yet to contain a Sasquatch that had recently gone on a rampage. But only Ti-yet realizes the reason for his old enemy's rage – the Sasquatch blames Ti-yet for the Lycanthrope massacre of the Sasquatch race, and he's looking for revenge.

Logan has disappeared. Sh'Lainn, looking for his whereabouts, finds herself at a Lycanthrope's hideout in which she sees a familiar face, but appearances can be deceiving. Not only must Sh'Lain confront Ruk's pack but also avoid the Conduit's forceful recruitment attempt of a young confused Lycanthrope.

Logan’s investigations and incarcerations have begun to feed his xenophobia – and his paranoia. After an argument with Sh’lainn, Logan finds a note telling him to “Seek your father in the conduit.” No information is available on the Condit, though it has over two thousand entries in the Alliance databases – all of which have been personally encrypted by Rinaker. Confined to quarters, Logan has no other choice but to escape to San Francisco and discover the truth about the Conduit, the Alliance, and a painful past for the Logan family.

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An Alliance flyer is picked up on radar, not responding to communications. But before the evidence can be destroyed, the Air Force captures the craft – and finds two caskets and dozens of small glass orbs on board. Perhaps this could explain the disappearance of Agents Logan and Fitzpatrick during an investigation and recovery mission to a voodoo controlled village in Haiti.