Voyager encounters a Graviton Ellipse, a massive body of subspace energy rolling through the galaxy. The crew suspects it may be the same phenomenon that caught and carried away an early Earth spacecraft in 2032, along with its lone human pilot, John Kelly.
They take the Delta Flyer into the energy body to investigate and hopefully find the long-lost spacecraft. Another spatial danger â determined to be dark matter â threatens the Flyer. Chakotay is ordered out but wants to bring the spacecraft with him. His disobeying of orders ends with the ship damaged, with no seeming way out before the Flyer is lost to Voyager.
Seven of Nine ends up beaming to the ancient spacecraft itself for spare parts. There she finds the body of John Kelly and footage of what he saw before he died. He had continued living for several days after the accident, until he shut down his life support because his engines had run out of fuel.
In the end, the crew is rescued and so is Kelly's body. A memorial service is held and Kelly's body is respectfully launched back out into space.