Captain Jean-Luc Picard awakens from a nightmare about his Borg assimilation experience to an incoming message from Admiral Hayes. Hayes informs Picard that Deep Space Five reported that a colony has been destroyed. Completing the Admiral's sentence, Picard realizes who destroyed the colony — the Borg.

Picard calls a meeting and informs his senior officers that their ship has been instructed to patrol the Neutral Zone. Their orders are to protect the area from any possible Romulan uprising during a Borg attack. Despite protests from his officers, Picard remains faithful to his orders and the U.S.S. Enterprise NCC 1701-E begins to patrol the area. Later, Picard regretfully tells Riker that it is his own fault they are stuck in the Neutral Zone. Starfleet believes Picard to be too emotionally involved with the Borg because of his previous assimilation to tactically complete a mission against them.

The men return to the bridge to learn that Starfleet has engaged in combat with the Borg. Intercepting messages between the starships, the crew learns that the Federation is losing. Picard, with his Borg experience, knows he can help the fleet. He informs his staff that he will make a decision directly in opposition to Starfleet commands. With no objections from his crew, Captain Picard gives the order and the starship Enterprise sets a course for Earth and the attacking Borg cube.

A massive battle ensues and it appears that the Federation will lose the fight. Despite serious structural damage to the Borg cube, their strength does not weaken. Even the U.S.S. Defiant, commanded by Worf, does not appear to be able to turn the tides of the battle. As the starship Defiant is about to ram the Borg ship on a suicide run, the U.S.S. Enterprise beams aboard its crew, including Worf. Picard, having an inside perspective of the Borg and their vessel, focuses the firepower of the fleet on coordinates he knows to be critical. Just as the main ship is destroyed, a spherical escape pod flies out. The sphere creates a temporal vortex, catching the starship Enterprise in its wake. Immune to the paradoxes created by the time travel, the starship's crew learns that Earth at the present time appears to be inhabited entirely by the Borg. The commanding officers realize that the Borg have gone into the past and assimilated Earth, so they follow them back in time to repair the damage the Borg have done.....