In 1991, HYDRA operatives in Siberia revive Andromeda Shun from a cryogenic state and condition him to be completely obedient to anyone who recites certain trigger words that can be used to turn him into Emperor Hades. He is then dispatched to assassinate a motorist and steal a case of super-soldier serum.
Approximately one year after Sweetie Bot's defeat at the hands of the Avengers, Pegasus Seiya, Pinky the Chihuahua, Cygnus Hyoga, and Pumpkin Cake stop Emperor Posseidon from stealing a biological weapon from a lab in Lagos, Nigeria. During the fight, Pumpkin inadvertently causes a building to be bombed, killing Posseidon and a number of Pride Landians relief aid workers and increasing the international community's distrust of the Avengers' work.
At the Avengers' headquarters, Secretary of State Granny Smith informs the Avengers that the United Nations is preparing to pass the Sokovia Accords, which will establish an international governing body to monitor and police the rapidly growing superhuman population. The team is divided over the act: Phineas Flynn supports oversight because he feels responsible for creating Sweetie Bot and for the destruction the android brought to Sokovia, while Seiya has lost faith in the government because HYDRA manipulated S.H.I.E.L.D. since its foundation.
In Vienna, where the Sokovia Accords are to be ratified, a bomb kills King Mufasa of The Pride Lands. Mufas's son, Simba, vows to kill the bomber. Security footage implicates Shun. Without authorization, Seiya and Hyoga track Shun to his hideout in Bucharest and attempt to protect him from the police and Simba. Seiya, Hyoga, Shun, and Simba are captured.
While in captivity in Berlin, Shun is released by Apollo, who uses HYDRA's trigger words to turn Shun into Hades and question him about the 1991 mission, then sends Hades on a rampage. Seiya stops Hades and sneaks him away. When Hades turns back into Shun and regains his senses, he protests his innocence and reveals that Apollo is heading to the facility where Hades and other Olympians were created. Seiya recruits Pumpkin, Perry the Platypus, and Ben Tennyson to help him. Phines convinces Ross to let him bring his renegade comrades in, and assembles Agent Pinky, Simba, Ferb, and Nightmare Moon. Feeling undermanned, Phineas visits Ezio Auditore da Firenze and recruits him as well. Phineas and his team intercept Seiya's team at Leipzig/Halle Airport. Agent Pinky lets Seiya and Shun escape, while the rest of their team is captured. Ferb is paralyzed after he is inadvertently shot down by Nightmare Moon.
Phineas discovers evidence that Shun was framed and secretly follows Seiya and Shun to the Siberian HYDRA facility, unaware that he is being pursued by Simba. They discover that the other Olympians have been killed by Apollo, who is Sokovian and wants to punish the Avengers for his family's death. Apollo then shows security footage that reveals that it was Phineas' parents whom Hades was sent to kill in 1991. Phineas, enraged and realizing Seiya's knowledge of the truth, turns on Shun. In the fight, Shun's cloth is destroyed, including the Andromeda Chains. During the fight, Seiya's cosmos reaches the 9th Sense, and he uses it to disable Phineas' armor, and has the chance to kill him, but decides not to do so. Seiya departs with Shun and leaves the Pegasus Cloth, that was turned into a God Cloth when Seiya reached the 9th Sense, behind. Apollo attempts suicide, but is stopped by Simba, who takes him in alive.
In the aftermath, Phineas gives Ferb an exoskeleton to let him walk again. Seiya breaks his comrades out of prison and flees to The Pride Lands, where Shun chooses to stay in a state called Elysium, where he'll keep sleeping forever unless someone wakes him up, until a cure for his brainwashing can be found. In a post-credits scene, Ezio is recovering from his injuries when his Hidden Blade project the simble of the Assassins.
- Pegasus Seiya as Captain America
- Phineas Flynn as Iron Man
- Agent Pinky as Black Widow
- Andromeda Shun/Emperor Hades as Winter Soldier
- Cygnus Hyoga as Falcon
- Ferb as War Machine
- Simba as Black Panther
- Pumpkin Cake as Scarlet Witch
- Nightmare Moon as Vision
- Agent P as Hawkeye
- Ben Tennyson as Ant-Man
- Saori Kido as Sharon Carter
- Ezio Auditore da Firenze as Spider-Man
- Emperor Posseidon as Crossbones
- Granny Smith as Thaddeus "Thunderbolt" Ross
- Apollo as Helmut Zemo