After being lured back to the hive during Voyager's mission to steal a transwarp coil, Seven of Nine is trapped on a Borg vessel. The Borg Queen informs her that the Borg "allowed" Voyager to liberate her from the Collective, but she won't be turned back into a drone because they want to study her memories. With her individuality intact, the Borg can look through her eyes to help them assimilate humanity. Meanwhile, Janeway discovers that Borg signals were being sent to Seven in her cargo bay alcove.
Determined to rescue Seven, Janeway leads an away team in the Delta Flyer to find the Borg sphere that took Seven away. They use the stolen coil to take the shuttle into transwarp space, and incorporate multi-adaptive shielding based on the Hansens' field notes from the U.S.S. Raven to go undetected by the Borg.
As Seven is given her first assignment to assist in the assimilation of a species, she secretly helps four of the individuals escape. The Borg Queen scolds her, saying that her human emotions of compassion and guilt are weaknesses that are causing her pain. However, when Seven pleads with her to let the getaway ship escape, the Queen grants her request.
After the away team follows the sphere into Borg space, Janeway prepares to send a message to Seven through her Borg interplexing beacon. The Queen gives Seven a new assignment — to assist in the programming of nanoprobes that will assimilate humans. The Borg plan is to detonate a biogenic charge in Earth's atmosphere, and Seven will be turned into a drone if she does not comply. Taunting her, the Queen reveals that one of the drones standing next to her is Seven's father. Suddenly, Janeway's signal comes through, and the Queen discovers it.
As the Borg adapt to Voyager's shielding, Janeway is forced to beam to the vessel and disable the shield matrix around the Queen's chamber. While Paris eludes the other ships, Janeway confronts the Queen and orders Seven to leave with her. A dispersal field is formed around the chamber to block the Delta Flyer's transporter beam, but Seven tells the Captain to target the power node above the chamber. This disrupts the Queen's command interface, and Janeway and Seven are beamed to the shuttle. They quickly enter a transwarp conduit, but not before a Borg vessel sneaks in behind them. On Voyager, Chakotay and Torres fire a full spread of photon torpedoes at the conduit threshold, collapsing it just as the shuttle bursts through. The Borg ship is destroyed, and Seven is home again.