Makoto, Adi, Chloe, and Bruno are teenagers who have been genetically modified and manipulated by Hydra to believe the Avengers are villains. After being deployed in the field, Adi and Chloe are horrified by the crimes they are forced to commit and decide to escape. They convince Makoto to join them and attempt to sneak out during the night, but are intercepted. Makoto manages to escape and flies to Avengers Tower, where Tony Stark is researching a Hydra initiative known as the "Emerald Rain Project". Despite his distrust of Stark, Makoto offers the location of Hydra's base in exchange for his friends' rescue. Stark agrees and departs with the Avengers for Hydra's base, detaining Makoto in the tower. At the base, Bruno reveals to the captive Adi and Chloe that he already knows Hydra is evil, and has sworn fealty to Red Skull.
Makoto escapes Avengers Tower and flies towards Hydra's base. The Avengers quickly dispatch Hydra's foot soldiers. Red Skull appears, clad in nanomachine armor, and begins to overpower the Avengers. Makoto arrives, and after he and Iron Man realize the nanomachines must be being controlled remotely, the two go to shut them down while the others battle Red Skull. As they storm the facility, Makoto finds his friends and asks Bruno to join them; Bruno refuses, as Hydra are the only ones who can keep his mechanical body from shutting down. Iron Man hacks Hydra's systems, opening the cells and shutting down the nanomachines. The Avengers defeat Red Skull, but the base's self-destruct is activated with the teens still inside.
Iron Man rescues the teens from the exploding base, while Bruno seemingly perishes and Makoto manifests strange emerald wings. The Avengers begin to suspect Makoto is tied to the Emerald Rain Project. The team is assigned as security during Red Skull's transfer to the Raft, accompanied by Makoto. Before they can interrogate him, the transport is attacked by the Winter Soldier, who has orders to eliminate Red Skull. The Avengers are able to drive him off with Makoto's help. Afterwards, Makoto demands to join the team, wanting to become a hero to honor Bruno's memory. Seeing the teens' resolve, and hoping to learn more about the Emerald Rain Project, the Avengers decide to train them to become heroes.
The Avengers pursue leads on the Emerald Rain Project and Winter Soldier, who is accosted by the Masters of Evil for his failure. Makoto, believing the Avengers are not taking their training seriously, convinces Chloe and Adi to sneak out and look for opportunities to practice their heroics around New York City. The three end up entertaining a group of local school children. When Avengers Tower comes under attack by Ares, the trainees stay to protect the kids, while their teacher, revealed to be Captain Marvel, leaves to confront the threat. When the school begins to fall apart, Makoto's Emerald powers manifest, allowing him to keep the kids safe. Iron Man, Hulk, and Captain Marvel defeat Ares, but Winter Soldier retrieves him before he can be captured. Later, Stark gives the trainees his new Visco gauntlets, capable of deploying their own weapons and battle armor, and Makoto dubs them the "Future Avengers".
Thor and the Future Avengers are invited by Iron Fist to the hidden city of K'un-L'un, as its elders have important information for the Avengers. While waiting to meet with the elders, Thor requests Iron Fist train the Future Avengers. He accepts, and has the three undergo a rigorous training regimen, using various chores to build their strength and refine their techniques. The elders tell Thor of a vision they received of cursed rain from green clouds and a light not yet strong enough to repel them, which Thor believes refers to the Emerald Rain Project and the Future Avengers. Enchantress infiltrates the city and animates its statues to attack. Using the lessons they learned, the Future Avengers help Thor and Iron Fist destroy the statues as Enchantress makes her escape.
Adi continues to have difficulty coping with the atrocities he committed for Hydra, believing himself unworthy of being a hero. Ezekiel Stane issues a challenge to Iron Man, seeking to avenge his father the Iron Monger. The Future Avengers learn of Stark's previous history in weapons development, upsetting Adi. Stane threatens to destroy the city with several unmanned Iron Monger suits, forcing Stark to accept his challenge while the Avengers protect civilians, with Adi rescuing a trapped girl. During the battle, Iron Man admits his guilt over his past mistakes, but refuses to let them define him, and defeats Stane. After the battle, Stark and Captain America reassure Adi that his past doesn't prevent him from becoming a hero.
