Season 2 Episode 11b, Orphan Substitute, wasn't actually meant to be the last episode in the entire series. Due to the events of 9/11 happening while Time Squad was mid-production, the fact that this episode made fun of president George W. Bush, and that Cartoon Network was going through changes in production at the time, the show was "quietly" abandoned by the studio.

According to co-writer Carlos Ramos, CN had told them the episode would never air, yet surprisingly he received a residual check for the episode years later, meaning it aired somewhere. (source)

A third season of TS was also reportedly in the works when it got cancelled. It is unlikely this show will ever air on CN ever again, much less get rebooted, which is a real shame considering how little content it has.