Chakotay, Kim, Paris and Neelix are taken hostage when the Delta Flyer is captured by a Borg Cube. However, it is inhabited by a small group of Borg children who were left behind, unworthy of re-assimilation. The underdeveloped Drones attempt to assimilate their captives, while Captain Janeway sends Seven of Nine to negotiate. After the Delta Flyer is intercepted by a Borg Cube, Chakotay, Paris and Neelix find themselves placed in what appears to be an assimilation chamber. However, Kim is not with them. A dead body lies on a table in the center of the room. It is partially assimilated and its face and arm are covered with implants that appear crudely inserted.
Meanwhile, Voyager discovers that the Borg Cube's propulsion system is off-line. The Cube first targets Voyager's warp core and then moves to its impulse engines. While the Cube's attack strategy is erratic and inefficient, Voyager capably disables the Cube's weapons. Seven discovers that there are only five signatures, instead of thousands of Borg, manning the vessel.
The Borg will return the crewmembers in exchange for Voyager's navigational deflector. However, Voyager will be unable to go to warp without it. Seven tells Janeway that the Borg most likely want Voyager's deflector in order to contact the Collective because their own is damaged.
While stalling the Borg, Janeway tells them that she is sending Seven over to make sure that her crewmembers are unharmed. Aboard the Borg Cube, Seven discovers that it is manned by neonatal Drones, children who have not matured long enough. The children insist that the Borg will come for them once their link is re-established.
Seven returns to Voyager along with a dead body of an adult Drone. She tells the Borg children that it must be examined in order to establish what went wrong aboard the ship. The Doctor discovers that a spaceborne virus attacked the Drones and is responsible for their deaths. The virus never reached the developing drones because they were protected within the maturation chambers. Malfunctions caused by the deaths of the adults led several chambers to open prematurely. The Doctor also discovers that if the pathogen is revived, it could be used to neutralize the Drone children.
The Doctor also discovers that a Borg baby has been transported to sick-bay as its systems aboard the cube would not sustain it. He tries to use this as an excuse not to use the pathogen, 'tricking' Janeway into holding the baby whilst he discusses his progress with the pathogen.
Because Voyager cannot give up its deflector, Janeway offers Seven's services in repairing the Cube's technology. One of the Borg children tells Janeway that she has exactly two hours before one of the hostages dies. Meanwhile, Kim wakes up after lying unconscious within the Delta Flyer and attempts to contact Voyager. And while speaking with the Borg children, Seven tries to jostle their memories in hopes that they will turn away from the Collective and come aboard Voyager.
While working on the Cube's repairs, Seven discovers that the Collective did receive the Drones' initial distress call and that they never dispatched a vessel to rescue them. The Collective declared the neonatal Drones irrelevant and damaged, severing their link to the Hive permanently. However, the Drone children were unable to decrypt this message, which stated that they are unworthy of re-assimilation. Meanwhile, Kim is captured and he awakes to raw-looking implants on his face.
By this point, 'First' (the unnamed leader of the Borg children) becomes so frustrated that he insists that Voyager turn over their deflector immediately. Seven tells the Drone children that the Hive will never come back for them and that their call for help was ignored.
Meanwhile, Voyager works to beam the hostages back by emittiing an energy pulse over the Borg Cube. Tuvok successfully beams Chakotay, Paris and Neelix onto Voyager. However, Seven and Kim are being held in a shielded area of the Cube.
Angered, First violently attacks Seven. However, his Second pulls him away. As the Cube's transwarp core begins to destabilize, Seven instructs evacuation. However, First refuses to leave, and is shocked and knocked to his feet. Seven comforts him while he dies. First's dying words are defiant to the last: "We are Borg."
Back on Voyager, The Doctor successfully removes the children's implants. Seven was able to salvage part of the Cube's database, which includes the other children's original assimilation profiles. Thus, the children discover that their names are Icheb, Mezoti, Azan, and Rebi.