The first half of the second season deals with the team facing Thanos, as he competes with them to obtain the Infinity Stones, followed by a five-episode arc detailing the return of Ultron, who plans to exterminate the human race. The rest of the season details the arrival of the Squadron Supreme and their confrontation with the Avengers.

In season 3, Ultron returns after his apparent demise and seeks revenge on the Avengers. The Avengers must defeat him as well as new threats like Baron Zemo's Masters of Evil and Kang the Conqueror. Vision, Black Panther, Captain Marvel, Ms. Marvel, and the Inhumans are also introduced.