Doctor Who: Flux is the closest viewers are going to get to a multi-Doctor story during Jodie Whittaker's tenure as the Doctor. Regeneration is the secret to Doctor Who's longevity. It means the show need never end; the moment an actor wishes to leave, the BBC simply cast a replacement. Even better, regeneration allows each portrayal of the Doctor to be different, meaning the show itself essentially regenerates with its star.
In 1973, Doctor Who's 10-year anniversary story united the first three incarnations of the intrepid time traveler - William Hartnell, Patrick Troughton, and Jon Pertwee. This multi-Doctor story was more than just a nostalgia fix; uniting the three Doctors allowed smart writing that showcased the show's evolution, and played the Doctors off against one another. Multi-Doctor stories swiftly became a tradition, and 1983's "The Five Doctors" was probably the best to date, even if it did require replacing the late William Hartnell with Richard Hurndall, while Tom Baker's unwillingness to return led to the episode using clips from a story that had never been broadcast. Modern Doctor Who has honored this tradition as well, with an anniversary special featuring David Tennant and Matt Smith's Doctors, as well as the late John Hurt as the War Doctor.
Sadly, it's clear Doctor Who: Flux is the closest thing to a multi-Doctor story viewers are going to get during Jodie Whittaker's tenure as the Doctor - in spite of the fact her story is ending with a BBC Centenary Special. Written by showrunner Chris Chibnall, Doctor Who: Flux episode 6 saw a strange cosmic event divide Jodie Whittaker's Thirteenth Doctor into three separate forms, essentially allowing her to have three different adventures at once. The episode was styled after "The Three Doctors," with two Doctors traveling around doing good while the third was imprisoned outside the universe, and it featured numerous explicit homages to the 1973 classic. All this meant it was coded as a multi-Doctor story, with Whittaker playing against herself.
Sadly, Doctor Who: Flux - as well as the three specials set to release in 2022 - were all shot during the coronavirus pandemic. As Chibnall has observed, this led to his Doctor Who; "Doctor Who is one of the most difficult shows to produce, and we were aware that [the pandemic] would make it even more difficult," he explained in an interview with Doctor Who Magazine. "I realized that there was a way to keep the ambition high - to move the show forward and to play around with things." This led to a single overarching narrative running through all six episodes, and a major benefit of this approach was that it featured more recurring characters - limiting potential exposure to infection. A multi-Doctor story would bring in several major actors, exposing production to new risks. Thus there won't be any true multi-Doctor stories during the Whittaker era.
This does not, thankfully, mean Jodie Whittaker won't potentially participate in a multi-Doctor story. Both Hartnell and Troughton left Doctor Who without appearing in a multi-Doctor story, only to return years later; in the same way, returning showrunner Russell T. Davies could well choose to call Whittaker back for a multi-Doctor adventure, giving her an opportunity to play alongside the as-yet-uncast Fourteenth Doctor - and perhaps even other incarnations of the time traveler. It would be great to see Whittaker honored by appearing in one of Doctor Who's multi-Doctor stories.