A mysterious organization contracts bounty hunter Nick Logan to capture Thrope, a dangerous fugitive. But Logan soon discovers that neither his employer nor his target are what they seem. The Alliance takes careful observations as they proceed towards recruiting Logan. His next assignment is to find Sh'lainn, a missing Banshee dissenter headed towards Roswell. But when Nick is unable to stop her before she gets to New Mexico, the Alliance decides that their secrets must be maintained - even if it means silencing both of them.

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Logan and Sh'lainn barely escape the Alliance's assault on the train they were taking to New Mexico. Now with a common foe and unanswered questions, the pair continues towards Roswell. However, the Banshee are hot behind them, intent on executing Sh'lainn for betraying the Clan. After a Banshee ambush, Logan must risk everything to rescue Sh'lainn.

When an Alliance team disappears in the Himalayas, Rinaker sends Nick and Sh'lainn to investigate without informing them that the top Alliance echelon had cut a deal with the Lycanthrope. In exchange for the Alliance tracking down the Yeti, former slaves of the Lycanthropes, Ruk guarantees that the werewolves and their Yeti slaves will leave the planet forever. But the Yeti are guarding a secret weapon stored in a mountain cache – and the Lycanthrope will do anything to get it back.

On July 4, 1947, a flying saucer was reported to have crashed near Roswell, New Mexico. This newsflash, and the immediate cover-up by the Air Force caused the perfect atmosphere of government distrust and conspiracy theories for the Alliance to hide behind. But, when the space shuttle is fired on by a cloaked Tribune satellite that has been monitoring North America for the past fifty years, Rinaker fears that the truth will be discovered about the Alliance's staged UFO crash. With both NASA and Intracom racing for the satellite and the secrets it's held for the past fifty years, the Alliance will have to capture an alien craft and prep it to destroy the satellite – all for the good of the people.

General Rinaker disappears on an investigation into an alien genetics lab, while mysterious cattle mutilations attract the attention of the Detection and Detail teams. Stranded in the middle of nowhere with an annoying temporary partner, Dr. Petrovic, Logan must find a way to stop the fused genetic anomalies that have been unleashed on a small town in Wyoming where everyone has disappeared.

Strange cattle behavior in South America convinces Rinaker to send Nick and Sh'lainn to find out exactly who, or what, is the mysterious Chupacabra. But to their surprise, the truth surrounding the identity and purpose of Chupacabra brings out details about an alien massacre at the hands of a shapeshifter posing as an Alliance operative, and the lost city of the Dark Empire.

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After a Lycanthrope breaks into Ti-yet’s prison containment cell and attacks him, Ruk is transferred to a high-security facility – and escapes Alliance custody on the way. Now teaming up with a former prisoner, Logan and Sh’lainn must stop the “civilization killer,” EMP bomb that has been recovered by Ruk’s pack.

Queen Mab releases the stasis fields holding two Minotauri warriors in suspended animation. They have only one assignment to complete if they wish to keep their freedom – bring the Banshee clan the head of Sh'lainn Blaze. But Sh'lainn won't stay in the protective confines of the Alliance Bunker. Her death visions show Nick being killed, and she won't let him die trying to protect her. Her only alternative is to flee the Minotauri bounty hunters… alone.

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When a Lyncathrope terrorist group takes over the Briarwood country club, Sh'lainn sides with a Lycanthrope defector during an Alliance mission to save the hostages. But, when the rescue mission goes sideways, Nick and Sh'lainn discover a deadly secret in the nuclear missile base underneath the country club.

Logan’s unauthorized search for Walter brings down the wrath of Rinaker, and reveals the true nature of Sh’lainn’s assignment as his partner. Logan pursues Intracom for clues, but as Logan and Sh’lainn dig deeper towards the truth, they unleash an extraterrestrial assassin.

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.

Mab, queen of the Banshees, disappears from the clan, and the Banshees suspect that the Alliance could be responsible for her abduction. Banshee warriors approach a renegade Sh'lainn and ask her to become their queen. Sh'lainn accepts and immediately makes her first decision as queen by declaring war on the Alliance.

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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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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.