The U.S.S. Voyager has entered a desolate region of space with no star systems in sight for two years, and the crew is slowly going crazy. The only activity in this vast expanse is some high levels of theta radiation. With nothing to distract her mind from its deepest thoughts, Janeway has retreated to her quarters and is agonizing over her past decisions that brought the crew to the Delta Quadrant. Suddenly, the ship loses power and is left in total darkness.
Once Kim and Tuvok get back partial power, they determine that a dampening field caused the power drain. Meanwhile, Paris is attacked by an alien in the holodeck, and Chakotay encounters one in the corridor. When emergency power is activated, three alien ships can be seen surrounding Voyager. They don't answer hails and begin firing until a larger ship forces them to retreat.
The pilot of the friendly ship, Emck, informs Janeway that thousands of the alien ships are ahead, but he can lead Voyager through a spatial vortex that will take them to the other side of the expanse unharmed. In return, he wants the alien they have in sickbay. Janeway questions the wounded "night being," who is dying of theta radiation poisoning. He explains that his people were living a peaceful existence in the void when the Malon began poisoning them. A course is set to take him home, and soon Voyager is surrounded by his vessels. As he is beamed back, the night alien pleads with Janeway to help them close the vortex and protect their space.
The crew observes the Malon ships are using the void as a dumping ground for their antimatter waste. Janeway offers Emck the technology to purify their reactant, but he refuses to cooperate because such innovations would put him out of business. A decision is reached to close the vortex, but it has to be done from inside the void. Janeway announces that the crew will proceed through the vortex while she stays behind in a shuttle and closes it, but her senior staff refuses to carry out orders to sacrifice her. Instead, they will close the vortex just after entering it. It will cause a major shockwave, but they are confident Voyager can make it to the other side.
As Malon ships begin firing, both of Voyager's engines are taken off-line. They continue toward the vortex to find a Malon freighter attempting to block their path, but night alien ships attack and distract it. Voyager scores a direct hit against the freighter then enters the vortex, deploying torpedoes to seal the entrance. The shockwave carries them to the other side, and the vortex is destroyed. Finally, Voyager emerges from the darkness into a star field full of light and life.