In the alternate universe, the Borg Collective has nearly collapsed against the forces of Species 8472. In a desperate move, the Borg Queen launches cubes to all parts of the galaxy to find a means of destroying Species 8472. When she encounters a fleeing Cardassian vessel, she assimilates the crew and discovers that the balance of power has shifted in the Alpha Quadrant, and sets out to Earth to find the source of power for this new Galactic Commonwealth and specifically the vessel stolen from another universe, the Defiant. After an assault on Earth the Borg Queen learns the means to travel to the Defiant's home universe and sends a vessel there to assimilate the information she needs to defeat Species 8472, information she discovers is held by the Doctor and a former drone, Seven of Nine. Meanwhile, in the Standard Universe, Admiral Kathryn Janeway and the Full Circle Fleet is tasked with traveling to the Borg Uni Complex, the former heart of the Borg Collective, and destroying it once and for all. When the Borg attack, the forces of the Full Circle Fleet, the Enterprise-E, the Aventine under Captain Dax, and ships from the alternate universe under their Captain Picard come together to stop the Borg Queen before she can unleash her new weapon on both universes.