Tony Stark/Iron Man serves as a mentor to genetically modified teenagers in *Marvel Future Avengers*. Researching Hydra's "Emerald Rain Project" when Hydra escapee Makoto arrives at Avengers Tower, Stark initially distrusts him but agrees to lead the Avengers in rescuing Makoto's friends in exchange for the Hydra base location. During the raid, Stark battles Red Skull in nanomachine armor. Recognizing the armor's remote control mechanism, Stark and Makoto infiltrate the facility's systems to disable it, enabling the Avengers' victory over Red Skull.

After rescuing the teens and witnessing Bruno's apparent death, Stark participates in transferring Red Skull to the Raft prison. When the Winter Soldier attacks the transport, the Avengers repel him with Makoto's aid. Observing the teenagers' determination to become heroes and seeking more information on the Emerald Rain Project, Stark and the Avengers decide to train them. Stark later develops specialized "Visco gauntlets" for the trainees, enabling weapon deployment and battle armor. Makoto names the group the "Future Avengers" following this upgrade.

Stark supports the team during training missions. When Thor takes them to K'un-L'un, Stark remains in a support role while Iron Fist conducts the training. The group later encounters Adi struggling with guilt over past actions under Hydra. Stark's history as a former weapons developer becomes relevant when Ezekiel Stane, seeking revenge for his father's defeat, attacks the city. Stark openly acknowledges his past mistakes but emphasizes they do not define his present, helping Adi reconcile with his own past. Stark then defeats Stane, reinforcing the lesson of possible redemption.

Stark continues providing tactical and technological support during Future Avengers missions, including investigations into the Emerald Rain Project and confrontations with foes like Ares and Enchantress, consistently leveraging his experiences to guide the next generation of heroes.