Janeway: "Captain's log, stardate 49678.4. It's been two weeks since the transporter accident that created Mr Tuvix, and while it's still not entirely clear that he's with us permanently he's certainly been doing his best to settle in. The crew seems to be growing accustomed to his presence and he's proving to be a very able tactical officer who isn't afraid to express his opinions. While he's forging relationships with many of the officers he seems to be keeping a respectful distance from Kes, allowing her to adjust to the circumstances on her own terms. As for my relationship with Tuvix, I've found him to be an able advisor who skilfully uses humour to make his points. And although I feel a bit guilty saying it, his cooking is better than Neelix's. My tastebuds are definitely happy to have him around."

Voyager flies at warp cruising speed in deep space, having left the planet

Tuvix, having just hung the picture in his quarters	Tuvix chats with a crewmember
Tuvix in discussion with Chakotay, and not afraid to express his opinion	in the Messhall, as Tuvix enters chatting with Kim, he notices Kes but does not approach her

Tuvix advises Janeway

Tuvix gets Janeway to sample a dish he has cooked; she finds it delicious!

Kim is practising the clarinet in his quarters when the Doctor contacts him on his personal computer. Doctor: "Sickbay to Ensign Kim. Please turn to your emergency holographic channel." At first Kim does not like being interrupted but he goes across and activates the com. channel as requested. personal computer on "How can I help you, Doc?"
Doctor: "Suppose I found a radioisotope that could selectively attach itself to specific DNA sequences? Could the surgical transporters be reprogrammed to lock onto those enhanced sequences and separate them from the remaining DNA?"
Kim: "Well, I think so, but we'd have to modify the molecular imaging scanners, and find a way to compensate for the higher levels of radiation." Doctor: "Thank you, Ensign."
He goes to end contact but Kim interrupts him. Kim: "Wait a second. What's going on?"
Doctor: "It's pure speculation at this point. I'll let you know when I've learned more." Kim: "This is about Tuvix, isn't it? I'm on my way!" He closes contact and leaves at once for Sickbay.

In the Chez Sandrine holoprogram, Tuvix is soundly beating Chakotay at pool. Tuvix is about to play and nominates: "Eight ball, corner pocket." He hits the white so that it hits the eight ball, making it roll straight into the corner pocket. "That's game again, Commander."
Paris jokes to Chakotay: "We've created a monster." Chakotay to Tuvix: "Best out of five?" Tuvix is about to accept when Kes enters and indicates with a head movement that she would like to talk to him. Tuvix goes over to Chakotay. "Would you mind if we finished this later, Commander? Chakotay, understanding that Kes wants to talk to him. "Not at all."
Tuvix and Kes sit down at a table together. Kes, a bit nervously: "Hi." Tuvix: "Hi. How have you been?" Kes: "Good days and bad days. You?" Tuvix: "Me too." Kes: "Listen, I'm sorry I've been so distant lately-" He interrupts. "Kes, you don't owe me an explanation." Kes: "I've been doing a lot of thinking, and I'm hoping that we can be friends." Tuvix: "I would like that very much."
Kes: "And I'd like our friendship to grow." She places her hands on his. Tuvix, welcoming the significance of the intimate gesture: "You would?"
Kes: "Yes. But it's going to take time." Tuvix smiles. "I'm not going anywhere." The com. signal sounds. comms. signal "Doctor to Lieutenant Tuvix." Tuvix: "Tuvix here." Doctor, via comms: "Please report to Sickbay immediately."

In Sickbay the Doctor displays information on his personal computer to the assembled group.
The Doctor explains: "Until late in the 21st century physicians administered barium to patients with certain gastro-intestinal disorders. The radioactive properties of the barium made the lining of the intestines visible with a primitive imaging technology called X-rays."
Kim: "Instead of barium, we've come up with a radioisotope that attaches itself to the DNA of one of the merged species but not the other."
Doctor: "Then we simply beam out the selected DNA and segregate the two merged species."
Kim fetches two flowers. "You see these? They used to be a single merged flower."
Kes, hopefully: "Then you can use the same process?"
Doctor: "It will require a more detailed reprogramming of the transporters, but yes I believe we can restore Mr Tuvok and Mr Neelix." Janeway smiles, pleased for Kes. Kes, realising that Neelix can be restored: "That's wonderful!" To Tuvix: "Isn't that wonderful?"
But Tuvix does not answer. He looks unhappy and sombre. Doctor: "I assure you, Mr Tuvix, there's nothing to worry about. We've accounted for every variable." Tuvix: "Except one - I don't want to die."
Janeway suddenly realises that Tuvix has become a problem. No one had anticipated this problem, and it raises a terrible dilemma.