Janeway orders Seven of Nine to assist the crew in removing the Borg modifications she made to the ship. However, while working, Seven accesses the subspace transmitter, trying to communicate with the Collective. But Kes senses her actions, and with her new enhanced abilities, she prevents Seven of Nine from completing the transmission.

Seven of Nine is held in the brig to prevent any further attempts to contact the Borg. Over the drone's objections, Janeway says she will make her fully human again, believing that the end will justify the means. Meanwhile, Tuvok becomes alarmed when he finds that Kes' new abilities are endangering the ship.

The ship's sensors reveal that Kes is periodically going into a state of cellular flux, with her atoms destabilizing at the subatomic level. Janeway is concerned but her attention is split by her efforts to help Seven of Nine, who is fighting against her assimilation into human culture every step of the way.

With the ship's defenses compromised by her transformation, Kes decides it will be best for everyone if she leaves Voyager to further explore her new state. Janeway barely gets her to a shuttle before Kes' molecules completely destabilize and she dissolves into pure energy. Kes uses her transformation to bestow a final gift on her Voyager family, hurling the ship safely beyond Borg space and ten years closer to home. The Doctor finishes extracting most of the Borg technology from Seven of Nine, leaving her with a human appearance and, Janeway hopes, the instincts to complete her own difficult transformation.