As the Avengers disassociate themselves with Truman Marsh, he assembles a new team Mighty Avengers (consisting of Red Hulk, Black Panther, Songbird, Ant-Man, Captain Marvel, Ms. After an increase of the Inhuman population done by the Terrigen Mist and the danger caused by them, Truman March enforces every Inhuman to abide by the Inhuman Registration Act that involves Registration Disks placed on them and orders the Avengers to hunt down any Inhuman who resist.

The storyline also follows an adaptation of Civil War, when the President signs the New Powers Act, the Avengers are given Truman Marsh as their government liaison who will be the one assigning missions to them. Marvel, Vision, and the Inhumans appearing this season. The Avengers must defeat him as well as new threats like Baron Zemo, the Masters of Evil, and Kang the Conqueror. In Season Three, Ultron returns after his apparent demise and seeks revenge on the Avengers. After Ultron's plans are foiled, they attack the Avengers with full force.

The Squadron Supreme has plans to become the superheroes of Earth and save the world their way. Thought to have perished when their old planet blew up, they survived and came to Earth in an attempt to conquer it with Hyperion re-joining their ranks when he hears of their survival. While Hyperion served as the 'Hammer' for the Squadron Supreme, Nighthawk served as the 'Architect' of the team. There is also a subplot detailing the arrival of the Squadron Supreme, Hyperion's old team from the same planet he's from which also consists of Nighthawk, Power Princess, Doctor Spectrum, and Speed Demon.

After the Avengers ultimately defeated Ultron, Ant-Man becomes a new member of the team. While the Avengers are able to defeat Thanos after much hard work, the gems are drained of their power by Ultron who threatens to exterminate the human race after possessing Arsenal's body. In Season Two, the Avengers face off against Red Skull's master Thanos (who Red Skull gave the Tesseract to at the end of Season One) who is on the hunt for the Infinity Gems to power his Infinity Gauntlet. Doom from conquering Asgard, Attuma driving the Atlantean Army into New York City or Dracula unleashing vampire hordes, the Avengers must work together to succeed no matter what. The planet's most dangerous villains don't stand a chance when the Avengers Assemble - whether they are stopping Dr. Led by Iron Man, the heroes train and live together in their new headquarters in Avengers Tower. Marvel's Avengers Assemble reunites the team, along with newcomer Falcon, marking the first time in animation history this distinct team of heroes will join forces. The record-breaking blockbuster film Marvel's The Avengers gave worldwide prominence to the most popular super hero team-Iron Man, Hulk, Captain America, Thor, Hawkeye and Black Widow.

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