Fresh from their vacation on Risa, the Nogura is ordered to rendezvous with a large ship traveling at slow speed in Federation space. Sent to make contact and establish a dialog, the Nogura encounters an alien vessel many times larger than anything in the Federation databases; almost 50 times bigger than any known ship. Starting their initial scans the object tractors the Nogura into the behemoth interior and begins to make the ship a part of itself, in effect assimilating the Nogura and her crew. Though the crew manages to get shields up, it's only a matter of time before the Nogura is forever trapped.

Sending out teams to explore the alien vessel, the crew find terrariums constructed for the thousands of other sentient beings captured and their descendants imprisoned. Many familiar and unfamiliar races are found, from across the Gamma and Delta Quadrants. Further, searching reveals that an AI, who calls himself the Collector, is responsible for the vessel's mission. The ship is eons old, traveling at very low speed (slower-than-light), capturing and adding aliens from ships and planets to its collection. The computers are degrading and have lost track of where it came from and why it's collecting.

While the crew seems to be powerless to escape, they opt to determine the nature of the Collector and help it and/or put an end to its mission while relocating the many intelligent beings aboard the vessel to new homes. Can the crew figure out this AIs plans and get their ship out in time, or will they be lost to the Collector for good?