When one of Voyager's probes is pursued by a Malon ship, Janeway orders that it be steered into a gas giant. After the Malon ship follows and implodes, it is obvious Voyager cannot go in to retrieve the probe. Paris has conceived a new technologically advanced shuttle — the Delta Flyer — that could withstand the giant planet's atmosphere, and Janeway gives him permission to work with the rest of the crew on building it. Meanwhile, Torres begins pulling away from the others. She activates a holodeck simulation of battle with Cardassians but disengages the safety protocols.
Another Malon ship approaches Voyager, and Janeway is hailed by an alien named Vrelk. He tells the Captain his ship is going to retrieve the probe, and she should stand down. She ignores his threats until Seven of Nine, using neutrino beams to spy on the Malon vessel, discovers they are building a shuttle of their own. It can also withstand the giant's atmosphere, and it's scheduled to be operational before the Voyager crew finishes their shuttle.
The crew steps up the pace of construction, and Seven's intelligence shows they are in a dead heat with the Malon to finish the vessels. When Torres runs a shuttle simulation in the holodeck to check for a fatal flaw, she once again disengages the safety protocol. The atmosphere of the gas giant begins to cause microfractures in the shuttle, and Torres is knocked unconscious. Just before the hull breaches, Chakotay arrives and freezes the program.
Once Torres is taken to sickbay, the Doctor finds old wounds that went untreated. Chakotay learns she has been running very dangerous holo-simulations without the safety protocols. When confronted, she admits she has been testing herself, trying to experience an emotion or feel pain. Ever since she and Chakotay received the Starfleet message telling them their Maquis friends had been slaughtered, Torres has felt numb. Suddenly, Voyager is attacked by the Malon, who are firing to create a distraction as they launch their new shuttle.
Janeway is forced to launch the Delta Flyer ahead of schedule and attempt to retrieve the probe first. Torres persuades Chakotay to let her accompany the away team. When the Malon begin firing charges at them, Seven's torpedo scores a direct hit, forcing them to retreat. Once Kim locks a tractor beam onto the probe, the shuttle begins losing structural integrity. Just as the hull breaches, Torres creates an ingenious device to trap the incoming gas in a containment field. The Delta Flyer returns to Voyager safely, and Torres is on her way to feeling whole again.