Voyager is under heavy attack from alien beings from another realm that are trying to preserve themselves from the Equinox's plans to use them to improve their warp drive. Chakotay is hit by one and collapses as Janeway reinitializes the shields. As Janeway heads for sickbay, Neelix hands her the mobile emitter he found on Deck Nine. The Evil EMH is activated and begins treating the injured Voyager crewmen. Chakotay wants to work on trying to communicate with the aliens to make them stop, but Janeway persists on trying to stop the Equinox.
On the Equinox, Captain Ransom is enjoying some R&R with the ship's synaptic stimulator when Lieutenant Burke arrives with Seven. Ransom offers Seven a choice; join the crew, or spend the two months it will take to get home in the brig. Seven chooses the brig. Ransom, obviously infatuated with Seven, asks Seven to reconsider. Later, when Burke is examining her, he discovers and reactivates Voyager's EMH. Burke leaves the two alone.
When the crew tries to add the alien compound to the enhanced warp drive, the engines fail. The power relays have been encoded, and it doesn't take long to find out who. Ransom demands Seven give them the encryption codes. She refuses. He then tells the Doctor extract the information. When he refuses, Burke deactivates his ethical subroutines. The Doctor immediately takes Seven away to begin the operation.
Voyager is prepared to try communicating with the aliens. They drop shields and send a message. An alien stops within two feet of Kim, hesitates, then returns to its realm. Then they start attacking Voyager again. The ship escapes, but Janeway is even more obsessed with finding the Equinox. Chakotay accuses Janeway of having a vendetta against Ransom, the man she once admired who left her to the wolves. Janeway not only admits it, but can find nothing wrong with it.
Equinox enters orbit of a
planet. Ransom sends an away team to the surface to mine for deterium.
Meanwhile the Doctor is about to begin the operation, despite all pleas from Seven. The Doctor will extract her cordical array to find the codes to the power relays, an operation that Seven will likely not survive. Ransom makes one final plea to Seven to give up the codes willingly. She declines.
Chakotay suggests to Janeway that they contact the Ankari, the race who introduced Ransom to the aliens. But since the Ankari are 50 light years in the wrong direction, she declines. She goes back to reading in Ransom's service record about his tactical tendencies.
Ransom is looking through his synaptic stimulator at a beautiful alien beach when he suddenly sees a woman in a pink dress. He's confused; he's never seen people with the synaptic stimulator before.
On the planet's surface, two crewmen are heading for the deterium source when suddenly they're attacked by Chakotay and Paris. The Equinox EMH contacts his ship and alerts the crew that Voyager has found them. Ransom tries to beam up the away team, but they're gone. He orders all hands to battle stations.
Voyager and Equinox exchange fire until Equinox loses its weapons array. Thinking quickly, Ransom orders the ship through the atmosphere, and Voyager cannot pursue.
Later, Janeway interrogates the Equinox away team. When they refuse to reveal Equinox's tactical status, Janeway threatens to drop the shields in the cargo bay and let the aliens have them. They still don't talk. When Chakotay realizes that wasn't a bluff, he defies orders and rescues the Equinox crewmen, he gets them to talk about the Ankari. There's a ship two light years away and Janeway reluctantly sets a course. Afterwards, she relieves Chakotay of his duties.
Voyager tracks down the Ankari ship and uses a tractor beam to get them to talk. The Ankari captain acts as a translator. The creatures agree to stop attacking Voyager if they can destroy the Equinox, and Janeway agrees. When Tuvok states she's acting irrational, she threatens to relieve him too.
Meanwhile, Ransom is feeling guilt about everything. First Burke says they need to kill more aliens than originally thought. Then catches the Doctor playing with Seven's auditory processor. He then puts on the synaptic stimulator. He sees the woman at the beach again-- it's Seven, sans implants. She tells him to put an end to everything.
Burke calls him away; Voyager's found them again. He recommends hiding in a nearby nebula, but Ransom says he wants to work things out with Janeway. Shocked, Burke pulls a phaser and orders Gilmore to take him to the brig. Burke contacts their EMH, asking him to relay their shield modulations to them.
As Voyager and Equinox engage in a high warp shootout, Gilmore takes Ransom to engineering and says they should work together to end this.
Voyager obliterates the Equinox's port nacelle and they both drop out of warp. Just as it seems Voyager's won, torpedoes start ripping through their shields. The Evil EMH's double agent tactics are working.
Suddenly they're hailed by Ransom, who announces his intention to surrender, but adds that Burke staged a mutiny. He'll do what he can to stop him. Changed, Janeway believes him. Ransom beams three of the Equinox crew and Seven back to Voyager and relays the Voyager EMH back to sickbay, where he deletes his evil counterpart and stops transmitting.
Realizing the tide has turned, Burke orders everyone to the shuttlebay, but the aliens attack en masse. Burke and the rest of the bridge crew are killed. Ransom is now the last one on board, but the core is about to breach and he has to steer the Equinox away from Voyager. He makes Janeway promise to get his crew home before the ship explodes.
With the aliens gone, life slowly gets back to normal on Voyager. Seven helps the Doctor install safeguards so his program can't be tampered with as it was on the Equinox. The five surviving Equinox crewmembers are stripped of rank, Chakotay is reinstated, and he and Janeway take the first steps in repairing their relationship.