During the "Opening Salvo" part of the "Secret Empire" storyline, Captain America, whose memory was altered by Red Skull's clone using the powers of Kobik, has a meeting with Roberto da Costa and tells him that he is no longer in charge of the team. Roberto then sees footage of the supervillain attacks in Manhattan, deep space, and in Europe. At the beginning of the takeover, Roberto assembles the team until he is attacked by one of his scientists who has allied with Hydra. He's later seen in a prison cell, nearly dead, by Red Hulk and Toni Ho. While adjusting to prison life, Toni manages to heal Roberto just in time when Hydra soldiers show up at their cell. Roberto then manages to use his powers to defeat the guards and free Red Hulk from the nanites controlling him, allowing them to take control of the prison. In the aftermath of the event, Roberto, during a meeting with the team's new congressional liaison in the White House, resigns from his position despite the objections from the senator. He then meets Izzy Kane, Cannonball's wife, who tells him that Cannonball, who went missing in action during the takeover and was presumed dead, is still alive on another planet.