Ahhh, Janeway's Victorian ("ancient England") holonovel. Set phasers to maximum twee! After some futzing about, she's interrupted by the news that a shuttle's been attacked, and Chakotay and Tuvok have been injured, and Chakotay is now brane dead.
Chaks and Tuvok have been hanging around together a lot recently. Might be something going on there, hmm? I'm just saying...
When Tuvok recovers, he says that a ship came out of a dark matter nebula and attacked the shuttle. Janeway decides to set course for the nebula. Shortly, the ship changes course again, but Paris doesn't remember doing it. Torres puts up a medicine wheel to help Chakotay. How are the stones sticking to the cloth sheet?
Kes says she senses a presence in her quarters. More strange things happen, and the HoloDoc analyses Paris' head, finding nothing wrong. Tuvok persists that he's the guilty party, despite the fact he can't remember anything. Then Torres initiate a warp core shutdown, and doesn't remember a thing.
HoloDoc finds something - memory tampering in Paris' brain at the points where he changed the course, and also in Torres' brain. He thinks an alien entity was controlling them. Janeway decides to turn the command codes over to the HoloDoc. After Kes mentions about her detecting a presence, Kim finds her and Tuvok knocked out in a turbolift.
Although Tuvok's all right, Kes is in a coma. During the meeting, Kim starts daydreaming, and everyone gets excited and thinks he's been taken over. Janeway is very disturbed that everyone's becoming paranoid.
HoloDoc reports that Kes was physically assaulted, and Janeway suggested that Tuvok may have done so while under the alien's control. Also, the HoloDoc's been shut down, returning the command codes to Janeway. After some more paranoid, a phaser fight breaks out on the bridge, ending when Tuvok stuns everyone.
After everyone recovers, Torres reports that the sensor logs on the shuttle had been deliberately erased, but she's recovered the data, and there was no other ship - the energy discharge came from the nebula. The ship reaches the nebula, and Tuvok says he's found the ion trail of the ship.
Then Paris reports that the injuries on Kes are consistent with the Vulcan nerve pinch. Janeway confronts Tuvok, who takes control of the ship at phaserpoint and flies it into the nebula. Harry says he's detected some life forms in the nebula. Tuvok says they are the Komar. In engineering, Torres is taken over by another alien and ejects the warp core. Janeways realises Torres doesn't have clearance to eject the warp core, and the computer says it was authorised by Chakotay, leading them to speculate the second alien is actually the disembodied Chakotay. WTF?
If I ever write Star Trek fanfiction, my Mary Sue will be a background ensign who has no lines, but carries around a sign saying "WTF?!" which he holds up at appropriate times.
They overpower Tuvok, resulting in the alien entity leaving him to return to the nebula, and struggle to find a way out of the nebula. Finally, Chakotay takes over Neelix and rearranges the stones on the medicine wheel to point the way, allowing them to guide the ship out.
The HoloDoc manages to "reintegrate" Chakotay's consciousness, and he wakes up.