Numbuh 101 appeared in Operation: Z.E.R.O., where he had Numbuh 1 and his team come to the museum for an "emergency" assignment which turned out to be delivering an ice cream cone to him, much to their annoyance. After they leave, he gives Numbuh 83, Numbuh 84 and Numbuh 363 a tour of the museum, which was interrupted when several villains launch a surprise attack, forcing him to call in Sector V once again. After the museum is saved, he tries to get Sector V's autographs in red, but they leave before he can get a red crayon.
Shortly after that, Numbuh 101 appears on the screen at the Kids Next Door Moonbase asking once again for Numbuh 1 and the rest of Sector V's autographs, and also revealing that the villains have stolen the Recommissioning Module, which he evidently does not consider as important as getting autographs, although the module was thought to be broken beyond repair, but had actually been repaired by Numbuh 86 in Operation: E.N.D.
After Grandfather put into action his plan to transform the population into Senior Citizombies, Numbuh 101 encouraged a depressed Numbuh 1 to use KNDNA Tracker to find Numbuh 0 and save the world. Later, he was seen as a Citi-zombie on the Moonbase, chasing a KND Operative and followed by a group of zombified hamsters are chasing them both. He reverted back to normal after Numbuh 1 defeated Grandfather and saved the world.
He was the only character who did not appear in The Grim Adventures of The Kids Next Door.He also didn't get assimulated by The Delightful Reaper.It can either be assumed he was unaware of The Delightful Reaper or he just came up with a good excuse to not appear in the crossover.