...But the Past Ain't Through With You is the second short story in the Apocalypse Suite era. It was released on Free Comic Book Day on May 5, 2007. The title is a line from the B-side track "Kill All Your Friends" by Gerard Way's band, My Chemical Romance ("And you can sleep in a coffin, but the past ain't through with you").
The story opens with The Séance, The Rumor, and Spaceboy standing over the dead body of The Rumor. The Séance scans the body and confirms it is indeed The Rumor, which confounds the team as to how The Rumor can be dead and yet standing next to them. Spaceboy gets a call from the other members of the team about a Sea Serpent in Japan.
Meanwhile the Murder Magician and The Assistant are on The Lucifer Clark Show, not only admitting to killing The Rumor, but unveiling their latest creation the Murderbot! Inspector Lupo waits outside the studio for the arrival of the Umbrella Academy, who have defeated the Sea Serpent and have come to handle the Murder Magician.
The team engages the Murder Magician and his Murderbot and The Kraken knocks out the villain, while Spaceboy, The Horror, and The Séance handle the behemoth. The Rumor kills The Assistant by saying that the catwalk she was attempting to escape on was unstable, causing her to fall to her death.
The Monocle arrives and questions his students on the mystery of the two rumors. Spaceboy deduces that Rumor created a duplicate when she lied and said she was at the library when she was sneaking out with a Polynesian Knife-Thrower. The Monocle then reveals he told the Murder Magician where to find her to teach her a lesson.