The Pathfinder Project uses a pulsar and the MIDAS Array, allowing a data stream to reach Voyager and Voyager to reply every 32 days. News reaches Voyager through the up-and-running Pathfinder that the Doctor's creator, Dr. Lewis Zimmerman, is critically ill. In an attempt to save his life, Captain Janeway authorizes the transmission of the Doctor's program to the Alpha Quadrant. Once there, the Doctor finds Zimmerman refuses to be examined by an "obsolete" EMH program and himself in danger of matrix degeneration.

Seven of Nine is led to a place known as Unimatrix Zero, a place where Borg drones are individuals for a short period during their regeneration. However, once their regeneration is complete, all recollection of the event is erased. Captain Janeway uses this to form a plan of attack that would create a mutiny instilling independent thought from within the Borg Collective.