In the wake of the horrific events of the 3rd Hellfire Gala, an Alpha Flight team is working closely with Orchis to subjugate and deport mutants to a warzone on Mars. Guardian, Puck, Snowbird, and Shaman may not be happy with the role, but they're following orders from the Canadian government. Opposing them are the original team's mutant members - Northstar and Aurora - plus Aurora's boyfriend Fang and a mysterious new Nemesis.
Alpha Flight provides examples of:
- Bait-and-Switch: At the beginning of issue 1, the team has a discussion about how conflicted they feel betraying the trust of the people they swore to protect. The implication is that they are talking about helping Orchis subjugate Canadian Mutants when in reality they are talking about their roles as moles within Orchis who are lying to the Canadian government about their true intention to help mutants.
- Bittersweet Ending: Nemesis teleports the Canadian mutants to Chandilar, in Shi'ar space, but falls into a coma; Argent (Laurent) dies; Alpha Flight is arrested and indicted with treason for helping the mutants. However, their story continues in the X-Force title.
- The Bus Came Back: Roger Bochs Jr., son of the late Alpha Flight member and student at the Braddock Academy, reappears for the first time since Infinity.
- Canon Character All Along: The third issue reveals that the new Nemesis is actually Heather Hudson, formerly Alpha Flight's leader Vindicator.
- First-Episode Spoiler: The ending of the first issue reveals that Guardian, Shaman, Snowbird, and Puck are all moles working closely with Northstar, Aurora, Fang, and Nemesis to keep the mutant citizens of Canada safe from Orchis and the Canadian government.
- Mecha: Box Sentinels, created by Roger, are Canada's answer to Feilong's Stark Sentinels. They're designed to be just taller than a normal human adult so that they don't cause collateral damage trying to apprehend mutants.
- La Résistance: Northstar, Aurora, Fang, and Nemesis are rescuing mutants from Orchis and the oppressive regulations of Canada. And the rest of Alpha Flight is secretly helping them.
- The Mole: The whole team are moles pretending to cooperate with Orchis so they can help mutants in Canada.
