Stardate 50252.3: During a shuttle mission Torres and Paris are attacked by an alien species that possesses transporter technology and neuro-electric weapons. Neelix warns that Voyager is approaching the territory apparently claimed by that species, a region in which ships have disappeared without a trace. Janeway decides to cross the border in spite of everything, because the shortcut would save 15 months of the journey home. Meanwhile in sickbay, the Doctor's program has started to degrade. Kes wants to avoid a total reset of the program, which would cause the Doctor to lose all his memories of the past two years since he was activated. So B'Elanna launches the diagnostic program, which turns out to be a holographic recreation of Doctor Zimmerman, who created the EMH at Jupiter Station. The diagnostic program tells her that the cause for the degradation is the accumulation of "nonsense" like friendships with the crew or singing arias in the Doctor's database. Voyager manages the evade the tachyon grid at the border of the alien species. Their ships form a large "Swarm" that so far doesn't react on Voyager's intrusion. Soon Voyager runs into a freighter that has been attacked by the Swarm, leaving only one heavily injured survivor. The amnesic Doctor is no help in treating the alien, who dies of his severe injuries. It turns out that one of the small Swarm ships has stayed behind. It attacks and causes a shift of Voyager's shield frequency that makes the ship visible to the Swarm. Kes tries her best to keep the EMH program running to slow down the degradation, but as the battle ensues no one is there to help her. She decides to expand the EMH using the matrix of the diagnostic program. Meanwhile, the Swarm has caught up with Voyager. Firing phasers on the Swarm is no use because the beam gets reflected. As Swarm ships attach themselves to the hull and drain energy from the ship, Janeway orders to destroy just one of the attackers while tuning the shields to the inverse harmonic. The other ships on the hull explode in a cascade reaction, and the Swarm retreats. After the repair it first seems that the EMH program has been reset, but then the Doctor begins to sing again.

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