A pair of Federation starships have been captured, with key information on recreating the transwarp portal. With Species 8472 in pursuit, the two vessels must be relocated to the nearest Borg Nexus immediately for disassembly and analysis. Progress is hampered by intense nebular activity.

Then, the Klingons have captured a Species 8472 bio-ship. In order to determine how the aliens are getting into the Alpha Quadrant, the facility analyzing the ship must be assimilated, and the Klingon forces suppressed.