A Galaxy-class starship, registry NCC-71099, the Challenger is commanded by Captain Geordi La Forge.

In an alternate timeline, where Commander Chakotay and Ensign Harry Kim were the only survivors of the U.S.S Voyager, the Challenger was dispatched to the Takara Sector to prevent those ex-Starfleet officers from changing history.

In 2375, after falling out of a quantum slipstream, Voyager had crashed on an icy, Class-L planet, just outside the Alpha Quadrant. The crash killed all aboard.

Chakotay and Kim — along with Chakotay's companion, Tessa Omond — conspired to steal a Borg temporal transmitter (Salvage Component 36698, found among the wreckage of a Borg Cube in the Beta Quadrant), as well as the Delta Flyer, from a Federation shipyard, and return to Voyager with the express purpose of violating the Temporal Prime Directive.

Upon intercepting the Delta Flyer, Captain La Forge was ordered to offer leniency to the outlaws, if they would stand down and turn over the Borg transmitter. They refused, so the Challenger had no choice but to fire upon the shuttle. Once the Flyer's engines were disabled, Challenger locked onto it with a tractor beam. However, Chakotay sent a plasma surge back through the beam, disrupting it, and allowing the Flyer to break free.