Alpha Flight vs X-Men

Alpha Flight is Canada's premier team of superheroes, which was organized under the auspices of the Canadian government's Department H. After the passing of the Super-Powers Registration Act at Parliament. The terms of the act entailed the government employment of all super-powered individuals, including Mutants. They are the top level of a three-tiered program; New recruits join Gamma Flight the next level up join Beta Flight. The active members in the field who where tasked with dealing with any threats to the nation were in Alpha Flight.

The Canadian government later resumed its funding of Alpha Flight, establishing for the team a headquarters on Tamarind Island off British Columbia. Over time, the relations between the government and the team grew strained. Canadian intelligence agent and Alpha Flight liaison Gary Cody searched for a way to keep Alpha Flight in line. He resurrected the being known as Bedlam, who was created by Hudson in an early Department H program to create superhuman beings. Bedlam killed Cody and destroyed much of Department H before violently confronting Alpha Flight. Alpha Flight eventually thwarted the villain and his agents, but the team was nearly decimated. In recuperating, the team found itself hopping from planet to planet and even dimension to dimension. When they finally returned to their reality, the team nearly caused an international incident in China. Alpha Flight effectively disbanded after this.

In Alpha Flight's disappearance, the government created a new Gamma Flight to replace the team. The two teams clashed, and Alpha Flight was forced to stand trial. Ultimately, Alpha Flight rejected the government's support and decided to operate independently once more. Gamma Flight continued as the government-sponsored team, and the two teams eventually met again to fight the evil Llan the Sorcerer. Gamma Flight was nearly destroyed in the final battle, but Llan was defeated. Afterward, Alpha Flight was again reinstated as Canada's official superhero group, with members of Gamma and Alpha Flights reshuffling into various levels of Beta and Alpha Flight, as per Hudson's original vision of recruitment.

Superhuman registration came to Canada, under the influence of the Master of the World in a civilian identity, restricting Alpha Flight's ability to operate. They eventually came head-to-head with the Master and his Antiguard, a newly resurrected version of James MacDonald Hudson. The Master was defeated, but Alpha Flight and Department H were left in disarray afterwards.

Later, Department H was reinstated by the Canadian government at unprecedented levels of funding. The Department sponsored many institutions, including an orphanage called Hull House. It also formed a new Alpha Flight, with an inexplicably teenaged version of Guardian leading the team. In reality, Department H was involved in many clandestine and criminal activities, unknown to Alpha Flight. General Clarke was the administrative head of Department H, who operated a hidden agenda and employed brainwashing techniques and Epsilon Flight guards to apprehend and coerce suspected traitors within Alpha Flight. It is unclear whether he had the official sanction of the Canadian government. Eventually, Clarke was opposed by Alpha Flight, but died a hero when Zodiac invaded Department H, so his crimes were never prosecuted.