Captain Janeway and security officers escort Tuvix into Sickbay, where the EMH and Harry Kim have prepared the transporter procedure which will kill him. The security officers continue to act like totally anonymous nobodies dealing with total strangers despite being isolated on the same ship of only 140 people for years.
EMH: I’m sorry, Captain, but I cannot perform the surgical separation. I am a physician, and a physician must do no harm. I will not take Mister Tuvix’s life against his will.
JANEWAY: Very well, Doctor. Please step aside.
TUVIX: You’re really going to do this.
TUVIX: No. Computer: Tuvix One.
Sickbay goes dark but for a transporter flare.
JANEWAY: Janeway to the bridge!
No response. The security guards grapple with the door, because “This has never worked in the history of ever” hasn’t been added to the tactical manual yet. They didn’t even open a little hatch beside it or anything. Janeway indicates and they fire phasers which flare against a forcefield.
BRIDGE: every console either blinks red or winks out
PARIS, hands raise from conn in surprise: Navigation just shut down!
CHAKOTAY, looking at that little armrest screen which must have some revolutionary new form of Federation-font which allows someone to administer an entire starship through five square centimetres of screen without squinting their eyes into neutronium: Every transporter system just overloaded and burned out.
KIM: Commander! The shuttlecrafts are launching!
CHAKOTAY: Which ones?
KIM, looks up dramatically, because that’s what you do when you’re meant to be keeping an eye on vital bridge readouts during a crisis situation: All of them!
EXTERNAL SHOT VOYAGER REAR: An infinite spiral of shuttlecrafts pour out of Voyager in every direction, a swirl expanding from the rear docking bay to blanket all of space in a solid mass of endless, unlimited, uncountable shuttlecraft. Their nacelles flare and the entire screen goes blue.
SICKBAY: The doors glow red and disintegrate under sustained phaser fire from the outside, the quarantine forcefield flaring out an instant later. Chakotay pokes his head through the hole.
JANEWAY strides towards the hole: What have you done to catch Tuvix?
CHAKOTAY shrugs: Nothing. You might not have noticed, Captain, but this whole quadrant’s a Skinner box training everyone that even saluting without your approval results in at least mutilation, second-degree glares, and three separate timelines where we all die. Last we saw of him was a hemisphere of shuttlecraft expanding in every direction away from the Alpha quadrant.
JANEWAY emerges into the hallway, seeing the entire remaining command crew sitting patiently in the hallway. Kim and Paris are attempting to act friendly, displaying all the natural warmth of a Breen and an Andorian scientifically measuring the freezing point of liquid hydrogen.
JANEWAY shakes her head, strides down hallway: Scan for his biosigns on those vessels and set a pursuit course.
TORRES pipes up: No can do, Captain. Sensors and weapons are offline, shields are raised and locked on, and the huge new Warp Core Override system sitting beside our warp core has us heading at maximum speed in the opposite direction.
JANEWAY stops: HOW in the name of Q did he install that there?
TORRES: Uh, he didn’t, he showed it to me in Cargo Bay 2. And I figured “Well, if we put intelligent warheads and hyper-evolved future-mutants right beside the most vital system in our ship, where else would I put this?”
JANEWAY nods as if to say “fair enough”, then turns: Kim, work with Torres to restore bridge controls.
KIM: Uh, captain, Seska was a Cardassian, and her cover was “loudly traitorous Maquis” with the rank of “sort of ensign”, and she still cracked our security like it was “PASSWORD”. Tuvok was our Vulcan Head of Security for several years. We couldn’t break Tuvix’s security if we ejected the computer core into space and fired a photon torpedo at it.
JANEWAY opens her mouth.
KIM: But the lockouts won’t let us. Even though the computer core would grow back by next week. There are already three new shuttlecraft in the launch bay, by the way. We still don’t know how that happens. But we can’t open the docking bay. We could pointlessly count how many photon torpedoes we have left to kill time if you like.
Voyager proceeds at maximum warp until STARDATE+RND*99, automatically returning control to the crew when it encounters an alien ship. The EMH reactivates to find that the radioisotope research has been deleted and replaced with the Hippocratic oath. Which has somehow been underlined and highlighted even when written in pure code. It’s also been linked to several ethical monographs on how if you develop a weapon, and tell someone about the weapon, then just sit there looking at it until they come and take it to use it, you’re not exactly doing no harm. He relays a message from Tuvix along the lines of “You’ll notice how I didn’t just kill all of you even in self-defense.”
Voyager eventually returns to Earth over a decade after their return in the original timeline. It turns out trying to murder your own chief tactical officer seventy thousand light years from the closest replacement isn’t a spectacular idea. They crew receive a glorious welcome, everyone on board receives promotions or generous Earthbound posts close to their family. Captain Janeway publicly declares her greatest task achieved and retires.
It is not publicly declared that she’s doing this to avoid the embarrassment of the Federation’s newest hero being tried for attempted murder based on a deposition submitted by Tuvix, who had crossed the Delta quadrant to use Gamma Quadrant wormhole several years earlier. Tuvix had not remained to press charges. Instead he broke the the news to Tuvok’s family – who dealt with it logically and without trying to kill him even once – before departing to continue his own life.