As Kim downloads the Borg’s tactical database, Kes is overcome by a vision of him screaming and tries to warn the away team. Back on the cube, Kim’s tricorder has picked up what he thinks is one of the unknown aliens. Just as Janeway orders the team to return to Voyager, the creature bursts through a wall, attacking some nearby drones before turning its attention to Kim who collapses in agony – just like in Kes’s vision.

Before the creature can finish him off, the away team is beamed back to the ship. The alien bioship detaches itself from the cube and prepares to fire on Voyager. As it does so, Kes – who has made her way to the bridge – has another vision, which she recognizes as the ship’s pilot communicating with her. As Voyager moves away, the bioship fires. It’s not a direct hit, but it’s enough to make them briefly lose control. Paris is able to make the jump to warp before it can fire again, and the alien does not give chase. As Voyager warps to relative safety, a visibly shaken Kes tells Janeway that it’s not the Borg she should be worried about, relating the alien’s message: “The weak will perish.”

After their escape from the bioship, Janeway heads to sickbay. Kim’s condition isn’t good. The alien cells left in his wound are basically consuming him from the inside out. To make matters worse, the Doctor can’t even sedate him. Due to the density of the alien’s cellular structure, anything that penetrates the cell membrane – be it biological, technological, or chemical – is instantly destroyed.

This, Janeway realizes, is why they pose such a threat to the Borg. Their biology is effectively immune to assimilation, and what they can’t assimilate, they can’t learn about.

Despite this, the Doctor believes that Borg technology may be their best hope of saving Kim. He explains that he may have found a way to reprogram Borg nanoprobes in a way that will allow them to attack the alien tissue. There’s a problem though. Even if this works, he only has so many nanoprobes to work with, and there’s no guarantee that it will be enough.

Meanwhile, Tuvok and Torres have managed to recover some of the Borg tactical data that Kim downloaded. The aliens they encountered are known (to the Borg, at least) as Species 8472. The Borg first encountered them five months ago, and have been overwhelmingly defeated at every encounter. They’ve also determined that the species originates in the Northwest Passage, explaining the lack of Borg activity. As if on cue, bioships begin to pour out of the quantum singularities in the Passage. As if things weren’t grim enough, Kes chimes in. Species 8472 has been continuing to communicate with her, conveying a sense of cold, malevolent hatred. She believes they are planning an invasion.

After moving Voyager to a safe distance, Janeway and Chakotay discuss their next move. Thanks to Species 8472, the Northwest Passage is no longer an option. The choice now is between facing the Borg on their own turf or turning back and in all likelihood giving up hope of finding a way home. While Chakotay remains optimistic, Janeway can’t bear the thought of telling the crew that the last three years were all for naught. Exhausted, she decides to try to get some sleep (for the first time in days). When that fails, she goes to the holodeck and presents a metaphorical version of her problem to Leonardo. When he suggests she accompany him to church and make an appeal to God, she realizes that the only way out may well be a deal with the devil.

In the briefing room, Janeway, well, briefs the bridge officers on her plan. She intends to propose an alliance with the Borg. In exchange for a weapon against Species 8472 (derived from the Doctor’s nanoprobe research), Voyager will be granted safe passage through Borg space. The crew is taken aback, but Janeway’s mind is made up. She further explains that all of the nanoprobe data will be uploaded to the Doctor’s holomatrix so that he can simply be deleted if the Borg make any attempt to threaten or assimilate Voyager.