Future's End

Part I

The crew is surprised by a small ship with a Federation signature which emerges from a temporal rift in front of the starship Voyager, and its pilot identifies himself as Captain Braxton (Allan G. Royal) from the 29th century. He shocks the crew of Voyager when he explains that he believes Voyager to be the cause of a temporal explosion which would wipe out most of the Earth's solar system in his time; therefore he must destroy them. As proof, Braxton briefly states that debris from Voyager's secondary hull will be found in the remains of the explosion. Voyager fights off Braxton's attack, resulting in the future captain being sent back through the rift to Earth in the year 1967. Voyager and its crew are also pulled into the rift and find themselves also at Earth, but in the year 1996. The starship is identified on Earth as a UFO and videotaped as such, placing the U.S. military on alert.

In 1967, a young hippie hiker, Henry Starling (Ed Begley, Jr.), finds the timeship and copies its technology, allowing him to create his own company, Chronowerx, and spark the micro-computer revolution. In 1996, a young astronomer named Rain Robinson (Sarah Silverman) who works at the Griffith Observatory in Los Angeles has discovered Voyager in high orbit through the ship's warp emissions and assumes it to be extraterrestrial life. Her work is funded by Starling, but against his instructions, she attempts to contact Voyager by transmitting a greeting to it, which forces the crew to do some damage control. The Voyager crew tracks her location to the Observatory and Captain Janeway, Commander Chakotay, Lt. Tuvok (Tim Russ), and Lt. Paris (Robert Duncan McNeill), decide to beam down to Los Angeles. Tuvok and Paris try to find Rain, while Janeway and Chakotay attempt to investigate more on the now multi-millionaire Henry Starling. Tuvok and Paris successfully remove Rain from the observatory before she can be harmed after Starling, who fears that Rain is a security risk, dispatches a hitman to kill her.

In Los Angeles, Janeway and Chakotay identify a homeless man as Captain Braxton. Braxton explains that he emerged from the time rift in 1967 and crash-landed in the desert, where a Henry Starling found the timeship and utilized its technology to begin his high-tech empire.

Ultimately, Janeway and Chakotay discover from Captain Braxton that Starling's planned attempt to travel into the 29th century using Braxton's timeship will be the true cause for the temporal explosion in the 29th century because Starling lacks the knowledge needed to properly operate the timeship. If Starling makes his trip to the future, the improperly configured temporal matrix will cause a temporal explosion that will destroy Earth's entire solar system. Braxton hypothesizes that Voyager's debris will be found in the remains of the explosion because they will try—but fail—to stop Starling.

Janeway and Chakotay decide to secretly enter Starling's Chronowerx office where they find the timeship, just as Starling walks in on them. Starling ignores Janeway's warning not to use the timeship since its use will cause disaster and he tries to kill Janeway and Chakotay, however the two are beamed aboard Voyager. When Voyager tries to beam up the timeship, Starling uses his own transporter beam to access Voyager's computer and study its systems before stealing the Doctor's program from Sickbay. Worse still, Voyager's presence is detected and placed on the news media since the ship's crew had to dive the ship low into Earth's atmosphere to beam Janeway and Chakotay aboard.

Part II

Janeway eventually manages to successfully abduct Starling and beam him aboard Voyager where he admits that he intends to travel into the future to steal more advanced technology. While Janeway believes that she has ended Starling's plans, one of Starling's henchmen uses his scavenged 29th century technology to transport Starling back to his office from where Starling launches the timeship to perform his intended time travel. After a failed attempt to convince Starling to stop his time travel before it's too late, Janeway destroys the timeship by manually firing a photon torpedo into it, destroying it just as it enters a temporal rift, and saving the future. An alternative Captain Braxton arrives, having detected their presence in the past, and returns them to their own time at the place they left it. He is unwilling to bring them to their Earth as that would violate the Temporal Prime Directive. In the process, the Doctor now gains more freedom as he keeps one piece of 29th-Century technology, a "Mobile Holo-Emitter", which allows him to move around without having to rely on fixed holo-emitters.