Voyager discovers one ship with one survivor. It tells of how the aliens covered every square meter of the ship, sucking out all the energy and killing the crew. The alien then dies of its injuries.
Voyager tries to get through the swarm's space but something is slowing them down. Phaser fire directed at the enemy is rebounded right back at them. Finally Kim finds a weakness. Each ship is connected in a lattice. Voyager concentrates fire on one ship, destroying it. Dozens of other ships are destroyed, driving the Swarm away.
Meanwhile, the holographic Doctor's program begins to malfunction. Kes and Torres transfer the Doctor to the holodeck and call up the EMH diagnostic program. This program is a holographic recreation of the Doctor's creator, Dr. Lewis Zimmerman. Both Zimmerman and the Doctor are identical.
The Doctor's program is threatening to degrade completely. The crew discovers they have the option of "rebooting" the Doctor if it comes down to it, but this would mean he would forget everything he had learned in the past two years. The Doctor is fine with this, as he does not wish to sacrifice the safety and security of the crew. The others, particularly Kes, do not wish to see the man the Doctor had become go away.
The diagnostic program itself is not pleased with the entire situation for many reasons. It notes that the Doctor was supposed to be off-line during its off time, not expanding his program, such as with his opera studies. The extra memory caused by all this is part of the problem. In fact, EMHs are supposed to only have 1500 hours of operation. The diagnostic program tells of an alternative to rebooting the Doctor entirely, but it involves a layover at McKinley Station. He is informed that the station is on the other side of the galaxy. Later, the diagnostic program expresses frustration over the situation, after all, it is perfectly content being the program it is.
In the end, the diagnostic program willingly sacrifices itself, using its matrices to support the Doctor's failing ones. This means the ship would no longer have a diagnostic system at all but it is better than the alternative, or so it seems. The Doctor is restored but acts exactly as he had when he was first activated. Moments later, while treating Torres's headache, he begins to hum opera.