Janeway's log opens with her stating that several weeks have passed and since Voyager is the only Federation ship in the quadrant, the crew have become more like an "extended family". Neelix has been serving his special recipes to the crew, to help save replicator power, but Janeway has been cut off from her regular black coffee and Neelix's "better" alternative isn't as attractive. After encountering a strange nebula with signs of omicron particles, Janeway orders: "Set a new course... there's coffee in that nebula", and the Voyager enters the nebula in an attempt to supplement its rapidly depleting energy reserves. En route to the nebula, Janeway asks Chakotay about the crew. He states that they're in a period of mourning, which is natural since there is no counselor, due to the original purpose of Voyager's launch. As they go through the cloud, the gases in the nebula are attracted to the ship's thrusters. They come across what appears to be a natural energy barrier keeping them 7000 km from the particles they need. Ensign Harry Kim engages thrusters to breach the barrier, which closes behind them.
Neelix, working in the kitchen with Kes, looks outside and sees the nebula. While he thinks it is a bad idea to go into one, Kes finds it wonderful to seek the unknown. As the ship enters further into the nebula, it encounters trouble when the shields begin to drop in power, reserves begin to fade, and the impulse thrusters trigger a dangerous reaction. Voyager leaves the nebula immediately, but now must use a photon torpedo to breach the barrier. The ship has sustained damage, and unidentified material from the nebula is attached to the hull. Torres and the Doctor investigate the material from the nebula: it is organic. They now realize that the nebula isn't really a nebula at all; it's a living organism. And by breaching the barrier, they have injured it.
The crew find a way to heal the nebula; the Doctor points out that it has a regenerative power, so they need only be a helping hand. Captain Janeway takes Voyager back inside to repair the damage done in the first encounter. Torres attempts to modify the engines to produce a suitable beam of energy, though the ship is more depleted than before. As they enter, the natural defenses of the nebula attack the ship more intensely, lodging it deeper and further from the wound. Chakotay finds a flow of energy in the nebula and believes it is the circulatory system. The ship reaches the injury using the "blood flow", initiates the repair, and leaves through the rupture before it finishes healing.
The Voyager crew must again search for an alternative means of resupplying power for ship functions. Fortunately, Neelix's knowledge of local space might lead them to what they need.
There are several side stories. Neelix appoints himself the ship's morale officer. Janeway receives help from Chakotay on finding her "animal guide" from Indian folklore: hers is a gecko (Chakotay says Torres once tried to find hers but then tried to kill it). Also, Lt. Tom Paris takes Harry to spend some downtime at "Chez Sandrine", a French bistro, with famous pool players, that he has recreated in a holodeck program. After the mission, Janeway and other crew members join them there to relax. Janeway adds a supplemental log at the end of the episode, taken from Chakotay's teaching: "Acuchimoya. We are far from the sacred places of our grandfathers and from the bones of our people. But perhaps there is one powerful being who will embrace this good crew and give them the answer they seek."