Stardate 48734.2: A shuttle with Tuvok and Chakotay aboard is attacked inside a dark matter nebula, leaving Chakotay without any bioneural energy - he is brain-dead. The Doctor says that he might be able to save Chakotay if he knew what kind of weapon was used, and so Janeway sets a course for the nebula. In the following, some unknown neural energy repeatedly takes control of crew members' minds and tampers with the navigation and propulsion system, obviously in an attempt to prevent the ship from entering the nebula. Janeway transfers her command codes to the Doctor because he is the only person aboard that can still be trusted. Kes too senses an alien presence and Tuvok suggests to help her focus her abilities through a mind-meld, but the two are attacked and Kes falls into a coma. Moreover, someone deactivates the Doctor and locks out his program. Janeway becomes aware that Tuvok lied. There was no attack with weapons but non-corporeal aliens have taken control of Tuvok's mind. The situation on the bridge escalates when Tuvok grabs a phaser and threatens to kill everyone. On his order the ship enters the nebula, where it is attacked by many alien beings. At the same time, however, Torres and briefly later Neelix are possessed by still another consciousness. It is Chakotay's. After disabling the alien in Tuvok with a magneton pulse that Torres had prepared to scan for the aliens, Janeway takes command of the ship again and follows a flight path suggested by Chakotay. The ship clears the nebula. The Doctor successfully reintegrates Chakotay's mind in his body.

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