Alpha Flight #1
"Omega to Alpha"
Sasquatch, Arachne, US Agent, and Talisman track a group of men trying to escape in a truck, after doing what we don't know. Sasquatch stops them cold but they have high-tech weapons and keep going. Omega Flight seems to have them cornered when one signals to US Agent, who then gets in his teammates' way, allowing the men to escape across the border into the States. Sasquatch correctly surmises they were SHIELD agents on a covert mission and that US Agent is working with them, at least implicitly. Walker abruptly quits the team and heads south himself. As the team returns to C.S.I.S. HQ Brown hears of the defection and acts relieved. With Weapon Omega dead and Walker gone, Brown reveals himself to be James Hudson.

Alpha Flight #2
"Walk this Way"
The women are told that Omega Flight and the C.S.I.S. directive were simply covers, while Department H and Alpha Flight retooled. Department H is shown to be under C.S.I.S. Sasquatch knew all along. More surprises are in store as Puck 'magically' appears and Nemesis is shown, too. Hudson retakes his role as Guardian. We learn that Hudson's cyborg parts kept him from the afterlife and Puck's savior was his mystic connection to Razaar. Guardian and Sasquatch believe Skrulls tried to wipe out Alpha Flight rather than infiltrate them, and that SHIELD is a Skrull haven. Meanwhile, erstwhile AF member Earthmover is seen in the company of...Brain Drain?

Alpha Flight #3
"No time"
Alpha Flight is fighting the Wrecking Crew again, and making short work of them this time. Eathmover is no more, we find out that his body has been taken over by Eshu, the Master, who is back in action and reforming the Hardliners. Talisman senses his existence.

Alpha Flight #4
Alpha Flight is attacked by a group of mercenaries lead by Mister M and Emme 'Cuckoo'. Alpha Flight is not amused and takes out the attackers with surprising ease. Both mutants turn out to be Skrulls. Soon after a SHIELD craft approaches and Nemesis says it's another Skrull-lead force; why do they want AF out of the picture? Meanwhile, the Master looks for allies.

Alpha Flight #5
"Left Turn"
The Skrull/SHIELD force is formidable, and it takes a massive spell from Talisman to drive them back. The team goes on the offensive and aggressively chases off the SHIELD force. Sasquatch determines that the Skrulls are afraid of something AF has: the mystic powers of Talisman and Nemesis.

Alpha Flight #6
Alpha Flight pursues the SHIELD force and brings it down. In the ensuing fight Alpha Flight tries to avoid humans and attack only Skrull infiltrators. Guardian finds that they may have to change their tactics as another SHIELD craft approaches. Nemesis tells Sasquatch to grab two particular SHIELD agents. Sasquatch threatens to rip them to pieces unless they reveal themselves. One chickens out and does so, to the amazement of the SHIELD forces. The Master has gained three new 'henchwomen': Persuasion, Pathway, and Goblyn.

Alpha Flight #7
"Let the battle be joined"
Alpha Flight officially joins the war against the Skrulls, with the knowledge that Skrulls can't hide from Nemesis.

Alpha Flight #8
"Turn around"
The Master tells his story of rebirth and power, believing that the utopia he desires is finally within his grasp. His Hardliners are a mix of super powered agents and armoured warriors. Alpha Flight has turned the tide in the Skrull war.

Alpha Flight #9
Nemesis is revealed to be the late Heather Hudson; she and Guardian have decided to leave their daughter with Heather's youngest sister and her family; it would not be right to try and take her back now anyway. Walter gets a visit from his teenage son, who reveals that he is just as 'golden' as his Dad, and hopes to join Alpha Flight someday, though not as Sasquatch. Walter is impressed by Isaac's intelligence and athleticism - seeing so much of himself in Isaac. Talisman gets a warning from her father.

Alpha Flight #10
"A Hard Place"
The Hardliners are making their presence felt, 'cleaning up' Canada. Alpha Flight is asked not to intervene as the Hardliners have government support. Department H only has AF, after all, and the Civil War is still causing problems for Canada. Guardian wants Alpha Flight to stay on top of the Hardliners. Talisman gets another warning.

Alpha Flight #11
"Who Calls?"
Arachne is attacked by a team of Hardliners but beats them off. She races back to Dept. H to tell her teammates what she's learned, that Persuasion and Pathway are on the other side. Talisman implores her team to look behind the mask of what the Hardliners are doing and see what is revealed.

Alpha Flight #12
Alpha Flight follows Talisman to northern Quebec, to a secret Hardliner base. As expected, they meet the Master. Alpha Flight are vastly outnumbered but refuse to back down. Talisman has a hard time handling the Master but Puck comes to her aid; seems he's immune to magic. And another surprise arises: Guardian is immune to mutant powers now. The Master and his forces hold their ground but take heavy losses. An injury to Arachne stops AF from pressing their advantage. At least now they know what they're up against.

Alpha Flight #13
Plodex technology has gained sentience and the Master races AF to confront it. The Master wins but finds the large being is hostile, carrying the race memories of the Plodex. The Hardliners withdraw. It's left to AF to deal with the menace.

Alpha Flight #14
With Arachne out of action the team has trouble; their chemistry is upset. They are soon joined by the lone Gamma Flight trainee, Burst, a non-mutant superhuman. His aid is welcome as it throws the Plodex creature off balance, allowing Guardian and Sasquatch to destroy it. Burst is upgraded to Beta Flight.

Alpha Flight #15
Alpha Flight makes a crucial decision: From right under SHIELD's noses they are going to destroy Apocalypse's safe houses. SHIELD is incensed at Alpha Flight's gall and Director Stark blurts out, "You should've stayed dead." Sasquatch surprises Stark by pinting out he knows SHIELD wanted Alpha Flight out of the way, and another surprise: mutants aren't the next evolutionary step from mankind, people like Burst and Valdez are. Mutants are an offshoot, like redheads, not evolutionary masters. The mutants at SHIELD take a dim view of Sasquatch's findings.

Alpha Flight #16
Sasquatch posits undeniable proof that not only was SHIELD complicit in the Collective's attack on AF but that mutants aren't the future of humanity. Guardian is a bit squeamish over how mutants will take the news, especially Northstar and Guardian, but he wants Department H to back Sasquatch up. Director Gentry agrees. SHIELD remains unamused, as do major mutant factions. Alpha Flight gets Arachne back and prepares for a rough ride. Burst is ordered to keep training, he's not ready for Alpha Flight yet, even if Arachne's daughter finds him cute.