When the X-Men discovered a young girl named Jubilee, Beast was in his lab when she saw him. While viewed by the girl, he expressed interest in some scientific endeavors and talked to himself. Once she started to roam around, Jubilee took out Wolverine while under the impression that he was trying to kill Gambit. Upon learning, he and Morph laughed together at their teammate before he revealed his claws, threatening the two. Jubilee left the Xavier Mansion sometime afterwards and was captured by a Sentinel. Learning of her captivity, Beast went with some members of the group to save her, where he expressed how his parents became aware of his powers. While the team moved closer to the Mutant Control Agency's facility, Rogue asked Beast what made them like they were. Beast gave multiple reasons and even brought up television as a possibility. Once Wolverine rejoined the team, Beast and Morph joined him in sneaking up the gate. With Morph needing a boost to get over the fence, Beast and Wolverine assisted him and were met on the other side by a guard, of which was soon taken down by Storm. Once the group made their way inside the building, Wolverine stopped the team once he smelled the inferred detectors. Beast asked him if he could sense them and learned that he was able to get their scent with his noise. Beast moved past the detectors by grabbing the ceiling's instruments and got the other side, of which allowed him to disable to the security systems. Once he got on the other side, he was joined by the rest of the team and prepared to open a door, which consisted of armed guards on the other side.
When the Friends of Humanity kidnapped Carly after her operation, Wolverine infiltrated their ranks and Beast started a mad rampage, determined to save his love no matter the cost. After the X-Men rescued her, Beast told her that he couldn’t see her any longer, as she was in constant danger when around him. He told her he hoped he would be able to return to her when mutants and humans could live in peace together.
Later, when Spider-Man came to the Xavier Mansion, Beast was the only one who understood the situation Spider-Man was in, having been there once himself. McCoy referred Spidey to an old friend of his, Doctor Herbert Landon, who was working on a cure for mutation. Little did Beast realize that his "old friend" was really working on a poison to kill all mutants, making humans dominate over mutants. Thanks to Spider-Man, Wolverine, Beast, and incidentally Hobgoblin, Landon’s scheme was foiled and Landon became a half-mutated creature as a reminder of the day.
