- Director of SHIELD, Peggy Carter, found to be a Skrull along with multiple other agents. The real agents are rescued from a Skrull spaceship within weeks after the discovery.
- Construction resumes on the Triskelion once the building is resumed; its lead scientists build a weakness into the prison after distrusting SHIELD leadership.
- Loki is charged for Kennedy's murder. This is a show to convince the Skrulls they have succeeded in scapegoating the Asgardian. Loki is 'killed' (December 11, 1963).
- Following Loki's death, protections around Earth allow Frost giants to roam.
- Loki comes back and reveals his true plans to take over Asgard.
- Multiple interruptions in the space-time continuum create chaos in Central Park.
- A war in Attilan sees Maximus removed as King of the Inhumans, with the Genetic Council resuming governmental control of the kingdom. The royal family itself was instructed to go out into the world and learn of the outside world, with the possibility of reinstatement at a later date.
- The Triskelion construction site is attacked by Sam Sterns. In the chaos James Buchanan Barnes escapes.
- Beatrice (Them! Plot) escapes from prison…
- The pandemic ends and no one seems to know why. Evidently the virus dismantled.
- At a protest the world learns that aliens are real once one dies (November 6, 1963)
- A taskforce (Act-F) devoted to resolving and planning for an alien attack is formed by Kennedy after acknowledging the reality that aliens exist.
- Kennedy is assassinated by aliens. Act-F becomes more important; Loki is accused of the murder (charges are pending)
- Bucky Barnes shoots Peggy (November 7, 1963)
- Peggy (SHIELD Director) is replaced by a Skrull (November 13, 1963)
- A new drug (Vigor) hits the street. It gives unpowered people powers and powered people a boost.
- A teenager from Hell's Kitchen is missing, but links to a much bigger pattern of missing powered teens. The police call them runaways, but ALIAS Investigations thinks otherwise.
- Wilson Fisk advocates for a powered police force to meet the recent slew of powered crimes, he gets traction and eventually gets his way.
- The Asgardians are outed and incur panic globally when Loki displays power on the Ed Sullivan Show (November 16, 1963)
- Construction begins on the Triskelion prison. Noteable prisoners include: Bruce Banner and James Buchanan Barnes.
- Giant bugs attack New York thanks to mutant activists. Eventually Beatrice, their master is imprisoned and subdued.
- The Avengers are disbanded thanks to pressure from US administration about having NATO operate a powered service on their soil (October 1, 1963)
- Weapon X is effectively disbanded after the government calls into question everything that it's done.
- The Hellmouth causes troubles across NYC as Dracula, demons, and Morgan LeFay try to enact their plans to create a bridge between Earth and Hell. Their plans are foiled and Morgan LeFay dies in a final standoff on Halloween.
- An illness that makes people's powers go berserk and prompts people to act with poor judgment spreads across the globe.
- A Science and Technology Conference sees partnership start in terms of science across East and West
- Mutants had been going missing from April - August; the X-Men rescue many when they learn these mutants are being experimented on
- A Hellmouth opens in Central Park as a result of actions to find people captured by Weapon X.
- Xavier's experiences chaos thanks to a giant living on its grounds
- SHIELD experiences a crisis whereby nuclear missiles have gone missing; MODOK swears revenge when they best him
- A special project, the Avengers, is formed. Slowly Captain America begins recruiting others for the project.
- Charles Xavier opens Xavier's Institute for Higher Learning.
- Charles Xavier and Erik Lensherr recruit the first mutant for the X-Men.
- S.H.I.E.L.D. (Supreme Headquarters, International Espionage, Law-Enforcement Division) officially formed with international oversight by NATO.
- SSR (Strategic Scientific Reserve) disbanded.
- Weapon X is created.