Menagerie Phase 2 continues the story told in the game, and in comics:
A teenage superhero team forms, and calls itself the Menagerie. The members are: Jason Quill (world hopping adventurer), Mercury (Harry Gale, speedster and son of speedsters), Ghost Girl (Charlotte Palmer, a specter from the Civil War), Link (Leo Snow, a troubled inventor), and Concord (Adam Amari, a younger teen invested with cosmic energies). Link also has two friends at the start: Otto (a transforming robot car) and Pneuma (a robot girl).
Jason is seemingly hunted by his nemesis, Alycia Chin, daughter of his father’s old enemy. In truth, Alycia’s motives are more complex, and she eventually joins the team as a full time member, replacing Jason himself.
The team learns of a parallel dimension called the Sepiaverse, marked by a lack of hope and a deterministic fatalism. They eventually discover that Byron Quill (Jason’s father) and Achilles Chin (Alycia’s father) are trapped there.
Rosa Rook, a powerful industrialist, attempts to kidnap Leo’s friend Pneuma. Along the way, she is split into two people: Aria (who experienced the trauma of the kidnapping and technological investigation into her systems) and Summer (who did not). During this time, Link learns that his father, the villain Rossum the Minion Maker, is secretly working for Rook.
The team repels a series of invasions from the country of Vyortovia, once known as Iceland. Along the way, Ghost Girl discovers her own connection to a secret organization called the Hidden Family of the Vyortovian Throne, and interacts with the emotionally unstable Magus Everard (who raised her from death).
During one such invasion, Concord is forced to fuse with his Concordance shard, Sol-Gamma-2, and gains access to a powerful cosmic asset, the Keynome. He must defend this against marauders from space such as Sablestar, of the Void Shadow Collective, and the Farlander.
The team visits a parallel future, sometimes called the Bad Future, the AltFuture, or the Quillverse. There, a future Jason Quill has disabled other members of the Menagerie and allied with Rosa Rook. He is defeated and comes to see the error of his ways.
On the way back from the future, the team is briefly trapped in a dreamscape, and it is discovered that Adam Amari has used the Keynome to create a variant present where his conflicted personal and superhero lives are more aligned - at the cost of the mental well being of some of his friends. The team deals with this.
The team has a final confrontation with a time traveling villain named Doctor Infinity, who has plagued them in the past (and the future…). They discover that Infinity is a time-traveling alternate Pneuma, and trap her in a stasis field for the time being.
The game sessions conclude with an alien invasion, from a species called the Blot.
The comics are more loosely canonical, but include visits from other parallel universes, battles against assorted supervillains, and Summer’s relationship with a boy named Colin.