Warning: This article contains discussion of misconduct.
John Barrowman's Captain Jack was a major part of the Doctor Who relaunch from 2005 onwards, even starring in his own Torchwood spin-off TV series, but he won't be returning. Introduced in the two-part story "The Empty Child" and "The Doctor Dances," John Barrowman's Captain Jack was a former Time Agent who'd turned into a cosmic con-man. He became a firm fan-favorite, and a regular throughout the entire Russell T. Davies era - even starring in his own spinoff.
Torchwood season 5 was put on hold after Davies' husband, Andrew Smith, was tragically diagnosed with brain cancer. Captain Jack himself would eventually be brought back by current Doctor Who showrunner Chris Chibnall in season 12, passing on a mysterious warning to the Thirteenth Doctor's companions in the episode "Fugitive of the Judoon." He then appeared in the 2021 Holiday Special, "Revolution of the Daleks," helping the Doctor break out of jail. Most viewers assumed at the time that Captain Jack would become a regular once again - but that's not going to happen.
In May 2021, historic allegations of misconduct were made against John Barrowman. He was accused of repeatedly exposing himself to co-workers during the production of both Doctor Who and Torchwood; although his actions weren't regarded as predatory, anonymous witnesses described themselves as feeling uncomfortable at his conduct. In 2008 Barrowman's actions put him on the radar of Doctor Who producer Julie Gardner, and she gave him a warning. Barrowman publicly apologized at the time, but when the issue resurfaced in 2021 the BBC clearly felt the need to cut ties.
A previously-publicized Captain Jack cameo was removed from the Doctor Who: Time Fracture escape room, and a tie-in Big Finish audio-drama Doctor Who: Absent Friends - which featured the reunion of David Tennant and Barrowman - was canceled. In an official statement, the producers of Doctor Who: Time Fracture declared their intention to "continue to include content that pays tribute to this brilliant show that is Torchwood so as not to disappoint its fans." More recently, a tie-in Captain Jack comic for Doctor Who: Flux was pulled as well.
Barrowman's position probably hasn't been helped by what seems to be a defensive attitude. In his view, the apology he issued in 2008 was sufficient, and in any case times have changed. "I think that if it was now it would be crossing the line," Barrowman conceded in an interview on ITV's Lorraine. "I think that something that happened 15 years ago – it was bawdy behavior, silly behavior." According to Doctor Who Production News, Barrowman has since accused the BBC of "blackballing" him, complaining he'd made them a lot of money but that he felt his loyalty hadn't been reciprocated. As such, Barrowman is unlikely to ever return to Doctor Who - meaning the story of Captain Jack has come to an end.