A bit of backstory before we get into the hypothetical: As we know, the French-Canadian actress was first cast as Janeway, but after two days of filming, it became painfully obvious that she was not right for the part (too quiet and subdued vs. Kate Mulgrew's confident and energetic performance) and that the part was not right for her (she had kids and couldn't handle the long TV hours). Looking back, it's a mercy that they realized this so quickly and dealt with it. But what if they hadn't? What if Bujold had toughed it out for, say, the abbreviated first season, then decided she couldn't do it anymore, resulting in them having to replace a lead, much like "Babylon 5" did? (This is setting aside things like contractual obligations and such). It's not as if you could have some new captain get assigned to the ship, like you could on any other series. I supposed you could have Chakotay inherit command, but it seems a shame to have Star Trek's only female lead be so short, and replaced by a man. Perhaps you could have some scenario similar to "Equinox" where they find another ship and captain, who promptly loses her ship and assumes command of Voyager, but seems terribly contrived. What do you think they would do?
Make an episode in which the captain and an until now never before seen crewmember "ensign X" get switched to another plane of existence. Both must be killed to return to their own plane (like Kim in Emanations). Unfortunately it turns out that the EMH can't repair all the damage. While he can save the captain's "engrams" and the ensign's body, conversely the captain's body is beyond repair and the ensign's brain activity is dead (but her brains themselves seem to be fine). So the EMH does the best he can, by transferring the captain's engrams to the body of the ensign (which of course turns out to be Mulgrew's). Not saying they couldn't have found a more imaginative solution, but to me this sounds like a solution the Voyager writers could employ
Let us all be grateful that Bujold quit and Mulgrew got the job instead. I haven't seen Bujold in any other movies or series so I can't judge her acting skills. Maybe she is a very skilled actress. But I don't think that she was the right person for the role of Janeway in Star Trek Voyager. Maybe she did realize that herself and it was therefore she quit. When I look at those video clips with Nicole Janeway, I find her rather woody and boring. The character lacks everything that Kathryn Janeway has in spirit, power and skills. I don't want to be rude but the only story I can come up with for Nicole Janeway is this story which is published on the Kes Website on the page "Voyager mysteries-and how to solve them: Nicole Janeway, who can be found on some Youtube clips instead of Kathryn Janeway is actually Kathryn Janeway's aunt. A sister to Kathryn's father Edward Janeway. Contrary to most members of the Janeway family, Nicole Janeway weren't interested at all in Starfleet and space exploring. She always considered her brother Edward a crazy fool who should have chosen another career instead of Starfleet. "Man doesn't belong into space", she often said. "It's utter foolishness to travel around in those metal boxes in such dangerous environment". When Edwards daughter Kathryn decided to join Starfleet, Nicole was furious. "You are a hopeless, reckless fool", she told Edward Janeway. "But worse is that you have raised your daughter to become one hopeless, reckless fool too", she said. And added, "This will end up in a disaster, believe me!" Nicole Janeway often expressed her compassion for Kathryn's mother Gretchen. "I really feel sorry for her, marrying my stupid brother" but expressed sympathy for Kathryn's sister Phoebe who had chosen to become an artist instead. When tragedy actually struck and Edward Janeway was killed during an exploring mission, together with Kathryn's fiancée Justin Tighe while Kathryn survived the accident, Nicole Janeway pestered everybody who wanted to listen with comments about "well, what did I say". Finally Phoebe Janeway got tired of hearing her aunt's complaints, lost her temper and told Nicole Janeway where to go. When Voyager dissapeared in the Badlands, Nicole Janeway continued to tell everyone (except Gretchen and Phoebe Janeway who had broken all contacts with her) that Kathryn only had herself to blame for being as foolish as her father. Due to her not too diplomatic comments about certain family members, Nicole Janeway became rather isolated from the rest of the family. She continued to live on her ostrich farm in Colorado while keeping her negative opinion about space exploring. The scene with Nicole Janeway as captain on Voyager was actually a nighmare Kathryn Janeway had two nights after Voyager left Ocampa, heading for the distant home. Only in a nightmare could Kathryn Janeway imagine her aunt as the captain on her ship.
It's interesting how they would have handled having to replace Janeway. Besides being a man, the trouble with Chakotay is he's made of wood. We aren't quite evolved enough as a people to have a wood Captain. They probably would have had to have Equinox style situation.
They could've just pulled a Saavik and recast without explanation. Or: "I've treated your facial injuries as best I can, Captain, but I'm afraid my cosmetic surgery subroutines were damaged in the attack. I couldn't quite recreate your original features." They could've done what Doctor Who's producers considered doing in "The Celestial Toymaker," and had Janeway's appearance arbitrarily changed by a capricious alien. They could've regained temporary contact with Starfleet long enough for a replacement captain to be sent through a wormhole or experimental long-range transporter or something. Or, heck, the experimental long-range transporter could've malfunctioned and scrambled Janeway's features. Or: Just establish that future cosmetic surgery is routine and easy enough that some people just periodically change their faces and bodies for the sake of novelty, like dyeing their hair or getting a tattoo. Although why Janeway would use ship's resources for such an indulgence would need explaining. Would an alien captain have been a possibility? It would take some doing to explain, first, why the crew would accept her leadership, and second, why she'd be willing to commit to the mission of getting the crew back to the Federation. They could've brought in the Borg earlier and liberated a Starfleet captain who was assimilated at Wolf 359. In which case they probably would've created a different, non-Borg character to replace Kes.
The face changing story reminds me of Logan's Run. As to cosmetic surgeries: the Doctor and other Starfleet CMO's have done cosmetic surgeries often enough (Sisko as Klingon, Riker as Mintakan etc.). Someone might decide to keep a "new" face instead of returning to the old after a mission.
It's harder to get away with recasting when it's the main character. I'm sure they could find any one of a million ways to put a new captain on the ship. "OMG, it's a wormhole. There's a shuttle coming through! It's about to explode! Beam out the one survivor! Hey, it's a Starfleet Captain! Oh darn, the wormhole closed." "Oh no, it's a Borg! We captured the Borg, let's remove the Borg implants. Oh, it's a Captain from Wolf 359!" "What the hell Q, why did you bring this random Starfleet Captain to Voyager?" "Oh we forgot to tell you, there was a Commander who has been in a coma since the start. She just woke up!" "I never thought...I'd see a Starfleet vessel again. Thirty years ago there was a space anomaly that stranded me in the delta quadrant. Oh I see you have a vacancy in the Captain position? But no...I couldn't...it's been so long...ehhh okay."
The '88 Superboy TV series did it (John Haymes Newton to Gerard Christopher). Filmation's Shazam! did it (Jackson Bostwick to John Davey). The Lone Ranger replaced Clayton Moore with John Hart for a season due to a contract dispute, then brought Moore back for the rest of the series. The syndicated The New Adventures of Robin Hood in the '90s recast Robin halfway through its 4-season run. (By coincidence, two other Robin Hood TV series, Robin of Sherwood and the 2006 BBC series, also recast their leads after two seasons, but they did so by bringing in a new lead character rather than recasting the same character.) Cagney & Lacey went through three different Cagneys in quick succession (Loretta Swit in the pilot movie, Meg Foster in the first six episodes, Sharon Gless thereafter).
Nicole Janeway is fatally wounded on an away mission, as she lies dying in sickbay she names Tuvok as her replacement. This usurping of his position leads Chakotay to lead a mutiny against Captain Tuvok, which sees him teaming up with the Kazon to exact his revenge, only to be defeated by Tuvok and the crew of Voyager. As the dust settles, Tuvok promotes the Beta Shift Watch Officer Lieutenant Elizabeth Palmer to Lieutenant Commander and First Officer and, to help smooth any possibly animosity between the two sides, appoints a former Maquis (I envision an alien female) as Security Chief.
A transporter accident results in Janeway's body being joined with another crew member, as what happened in Tuvix. There would be some physiological complication that would make separating the 2 impossible. Of course it would be challenge to cast the 2 roles. They'd have to cast a new captain that bears some sort of resemblance to both Janeway and the previously unseen crew member (with a stellar Starfleet record) she merges with.
Janeway gets infected by an alien pathogen. As a result, her DNA is modified, not obliterated, and she morphs into a slightly different being. She looks different, has some new quailites but has retained her old self as well. Sort of like a trill, but there is not a seperate symbiant. A few episodes could be devoted to the crew deciding whether not not she should maintain command, and if they have full trust in her. They discover that, rarely, an alien on the planet where the pathogen originates can become infected as well. It is rare becasue it only occurs when a very specific set of conditions and genetics occur, but when it happens, the person infected always becomes smarter and develops some other positive attributes, so in their culture it is considered a gift. The doctor can't understand it or reverse it.
After Janeway is killed in the line of duty, Q pops in with Amanda Rogers who has decided to give up her powers.
A previously unseen crew member steps forward. She is an admiral who had been working undercover, and had information and proof that Janeway is not what she seems to be. The crew is in shock to find out that Janeway has gone rouge and intentionally stranded the ship in the Delta quadrant as part of of some task for the Romulans. They decide to let Janeway live under house arrest and the admiral takes over command. Janeway steals an shuttle and gets away. The Enterprise runs into Janeway a few times over the next few years.
I guess I have to come up with a story where Nicole Janeway is abducted from her remote ostrich farm by some unknown aliens and Janeway goes out on a mission t rescue her.
I like this scenario where Tuvok finally gets what is rightly his due, the Captain's chair. Sorry but I cannot imagine Chakotay taking this position. Not given his past and his opinion about Starfleet, which doesn't seem to have changed in 7 years although he accepted, compelled and forced, to wear a Starfleet uniform again.
Thank you @Ghislaine H. B. BRAEME. I've never been overly fond of Chakotay and couldn't see him in the Captain's chair, whilst Tuvok is a far more nuanced and understated character who never got the love he deserves. He'd approach his new position with logic but also seek to keep the spirit of his long-time friend alive and fulfil her drive to get the crew home. As for the new additions, it'd help keep a woman in a senior role and add a little more alien diversity (plus also the question mark over his decision to appoint a former Maquis as his replacement might add a little tension in the beginning).
I am fond of Chakotay, but given how he was written...acted..something...in this time line I don't see him as a Captain . Not without some character growth.