Ben tags along for all of Klaus's adventures in season two, quite fed up with watching his brother string along his followers and run away from his responsibilities. He continually attempts to possess Klaus's body, finally convincing him to let him take control so he can spend the afternoon with a follower named Jill. His afternoon of corporealness doesn't last long, though. Soon after, Ben finds himself tagging along as Klaus, Diego, and Allison attempt to retrieve Vanya from the FBI. Because of the force of Vanya's power blast, his other siblings are unable to reach her, leaving Ben to try and snap her out of her trance. He does so, but in the process, Vanya's power eats away at his spirit, "killing" him a second time. Before he ascends, he asks Vanya to tell Klaus that Ben chose to stay with him and it wasn't his fault he hadn't descended.
At the end of the season, the six siblings travel back to 2019, only to discover that their home has been changed. Sir Reginald is alive, the Umbrella Academy has been replaced by the Sparrow Academy, and Ben is alive. (Though, much more emo looking than we're used to.)