The Cybermen are incredibly prominent in Doctor Who lore, so although it's disappointing the show failed to give Ncuti Gatwa's Fifteenth Doctor an episode featuring the mechanical villains, the franchise did quietly allow that encounter to happen. Huge portions of the fan base probably missed it, but it's definitely worth seeking out.
Ncuti Gatwa's era of the show lasted just two eight-episode seasons and two Christmas specials. The BBC's partnership with Disney brought with it a huge overhaul that has left many fans (and certain figures involved with the show) with the opinion that Doctor Who is due for another hiatus.
Arguably, part of the reason for the perceived dip in quality during Doctor Who's Disney era is returning showrunner Russell T Davies' decision not to give Fifteen a run-in with the Cybermen. Such an encounter is viewed as something of a rite of passage for most Doctors. However, Fifteen DID have a story built around the Cybermen, and it was a very good one.

The Fifteenth Doctor faced the Cybermen in the Doctor Who comics
Gatwa's first season as the Doctor began in May 2024 and ended in June of the same year. Just before the run ended, Titan Comics released the first of four issues that would go on to be collectively known as Everyone Must Go! It concluded in November 2024, and heavily featured the Cybermen — albeit as secondary antagonists.
While the Cybermen that Fifteen faced in the comics turned out to be a creative spin on the iconic Doctor Who bad guys, the more recognizable form of the Cybermen also played a significant role in the story. With Gatwa stepping away from the show after his 2025 regeneration sequence, it now seems likely that Everyone Must Go! is the only Doctor Who story that will bring his Doctor into close quarters with the Cybermen.
Still, that's not necessarily a bad thing. Comic books might not be for everyone, but for those who pick up a copy of Everyone Must Go!, they're not going to be disappointed. The story feels very authentic to the show and even makes sure the reader knows it's set just after "Rogue," which was the episode that introduced Jonathon Groff as Fifteen's new love interest. I struggle to imagine how Doctor Who could make Fifteen vs. Cybermen better than it already did in Everyone Must Go!

Fifteen vs. the Cybermen is (sort of) what Gatwa wanted all along
In an interview with Entertainment Weekly before Gatwa's first Doctor Who season premiered, the actor spoke about speculation that he would never meet the Daleks during his time as the Doctor. He said he would be "so angry" if that turned out to be true. Sadly, it was, and Gatwa missed out on facing the Daleks altogether while leading the Doctor Who cast. As of yet, it hasn't even happened in the comics.
Even though Gatwa's Doctor never got to meet the Daleks, going toe-to-toe with the Cybermen is probably the next best thing. The adventure may not have directly involved Ncuti Gatwa himself, but his comic book equivalent is understandably influenced very heavily by the actor's physical appearance and personality when he embodies the role. You can almost feel Gatwa jumping off the page.

"Everyone Must Go!" doesn't just focus on the Cybermen
The Cybermen's presence certainly makes the Fifteenth Doctor comic feel like it slots perfectly into Doctor Who canon, but the comic doesn't neglect its duties as part of an ongoing story arc from that time. The Pantheon of Gods was a huge part of Gatwa's era, and that's no different in Everyone Must Go! Writer Dan Watters introduces a new and terrifying member of the Pantheon known only as the Scream Sommelier. As the name suggests, the villain collects rare and interesting screams in bottles that look built for storing vintage wine.
He might sound a little silly on paper, but that's often the sign of a good Doctor Who villain. The Scream Sommelier — presumably the Pantheon's God of Fear or Screams — is confirmed to originate from outside the universe, and even threatens the Doctor with the imminent arrival of "The One Who Waits," who we all now know is Sutekh. The connection between the Cybermen and the Sommilier is brilliantly executed, and ties the comic's entire story together.

Is it too late for Gatwa's Doctor to face the Cybermen in live-action?
The issue with Doctor Who comics, or any story that happens away from the screen, is that they generally aren't part of the main canon. They're often written to make sense and as though they are part of the same continuity, but they really need to be referenced by the show for this to be true. So, it's not actually official that Fifteen has faced the Cybermen...yet.
With Doctor Who currently in limbo, the topic of when it will return is being hotly debated among fans. I'm sure it will come back eventually, but when it does, Gatwa has already left as the show's star. Billie Piper's confusing return as maybe-not-the-Doctor means Fifteen's time in the TARDIS is done for now. That said, there's nothing really preventing his return at some point.
Actors who have previously played the Doctor return to the show on a relatively regular basis. This is proven by David Tennant's comeback as Fourteen in 2023, and even Jo Martin's recent cameo as the Fugitive Doctor in 2025's "The Story & the Engine." So, if Ncuti Gatwa were to return as Fifteen for a special or a multi-Doctor story, Doctor Who could finally give his version of the Time Lord an on-screen battle with the Cybermen.