The U.S.S. Voyager is pulled into a void with no apparent way out. Neelix presents an exotic dinner to Janeway, Chakotay, Paris and Torres, a meal prepared by Seven of Nine who is trying her hand at being a gourmet chef. Suddenly the ship jolts and a graviton surge pulls them toward a swirling funnel, and they wind up in a realm of complete blackness. Then, an alien ship begins firing upon them. As Voyager fires back, a larger ship swoops by and fires at the other ship. Then the second ship fires at Voyager, penetrating their shields, and transports several cargo containers, food, deuterium and other supplies from Voyager to their ship.
Another ship approaches Voyager and an Annarian named General Valen appears on Voyager's viewscreen, welcoming Captain Janeway to "the Void." Coming aboard, Valen tells Janeway that Voyager was sucked into an inert layer of subspace, nine light-years wide, through one of its "funnels." Valen and his ship have been in the Void for five years, and no one has ever found a way to escape from it. In order to survive, the trapped ships compete for resources from new ships that are drawn in.
Torres reports that the anomaly's graviton forces are draining the warp core, and they will run out of power in 10 days. Seven, Tuvok, Paris and Janeway come up with a plan to enter a funnel and jump to warp at exactly the right moment to escape. Implementing their plan, they peer through the eye of a funnel and prepare to jump warp. However, the eye suddenly closes and the funnel shoots Voyager back into the Void. Torres reports that the warp core is now off-line.
Torres thinks she can fix the warp core, but they need the deuterium that was stolen from them or basic systems won't last more than a week. Janeway gives orders to track down the ship that raided them and get back their supplies. They find that ship, but detect no lifesigns on it — apparently it was raided as well. However, one piece left behind — the ship's warp core casing — is composed of tricesium, which can be converted into a power source. Voyager beams the casing over, and when Seven and Torres scan it they find a small alien inside. The timid creature does not speak, and has a leg injury. In Sickbay, the alien won't let the Doctor close enough to treat him, and he eats voraciously. Janeway and Seven wonder why they didn't detect the mysterious being, but decide to make him comfortable until they can find a safe place for him.
Meanwhile, Tuvok and Harry Kim discover that General Valen raided the lifeless ship and now has Voyager's supplies. Janeway contacts Valen and demands the supplies back, but he refuses and the two ships exchange fire. Voyager manages to transport back about half of their stolen resources, and an opportunity presents itself to raid Valen's ship for additional food, but Janeway declines to do that. Later, Tuvok and Chakotay approach Janeway and suggest that the crew may need to be more opportunistic in order to survive in the Void. Janeway points to the Federation Charter as a statement of principles that they should not abandon. Using the Federation model of mutual cooperation, Janeway proposes forming an alliance with other ships to pool resources and devise a way to escape, on the condition that members of the alliance not resort to killing or stealing.
Janeway's first prospective ally is a Jelinian survey ship with a captain named Garon. Skeptical, Garon says he will consider her proposal. Janeway continues to make overtures to a ship of Nygeans and other potential alliance members. Meanwhile, the Doctor realizes the mute creature in his Sickbay loves music, and has named him "Fantome" after "The Phantom of the Opera." Seven gets the idea of trying to communicate with the alien by way of computer-generated tones, and Fantome responds enthusiastically.
A funnel opens in the Void and another ship is pulled in. Two warships approach, including Valen's, and try to attack, but Voyager defends the newcomer. About to lose the battle, Voyager is joined by Garon's ship and forces the raiding vessels to retreat. Garon hails Janeway to accept her offer of an alliance.
With Garon on board, finding new allies becomes easier. Janeway hosts a visit by Commander Bosaal whose ship has technology that could aid in an escape. But he reacts adversely upon seeing Fantome in the Mess Hall, accusing his species of being vermin. Janeway tells Bosaal that they've figured out how to detect the creature's lifesigns and can transport those of his kind off his ship. With that, Bosaal agrees to be an ally.
Torres works with Garon to build a polaron modulator that will help the alliance ships escape the Void, but so far they have failed. Janeway hopes to trade with another ship for a polaron modulator. Meanwhile, Fantome joins others of his kind in learning how to communicate through tones generated by PADDs, creating a musical "conversation" that amazes Janeway. Later, Janeway learns that Bosaal has provided a fully compatible polaron modulator, but pressing him on how he got it, she realizes he stole it from another ship and killed its crew. Enraged, Janeway orders Bosaal off the ship along with the modulator — although the technology would help them escape, she refuses to be accessory to murder. As a result, some of the other ships drop out of the alliance, and Torres has to continue trying to build a modulator from scratch.
Later, one of the remaining allies spies on Bosaal and discovers that he is attempting to form an alliance of his own with Valen and other adversaries, with a plan to attack Voyager. Without the resources to defend themselves, Janeway realizes they need to make an escape attempt right away, even though Torres hasn't had time to test her new modulator. The ship readies its plan with its allies, and Fantome's people — who are native to the Void and live as nomads on ships — want to help out. When a funnel is detected, the alliance ships prepare to go in. Bosaal and his fleet approach and begin firing. Firing back, Voyager manages to penetrate shields on two of the ships and transports Fantome and his friends over. Seconds later Fantome hails Voyager that they have sabotaged Valen's ship; Bosaal's vessel has also been disabled. That gives the four alliances ships time to enter the funnel in a "shield bubble" and jump to warp to enter normal space. The successful allies then wish each other well and go their separate ways.