|"Secret Shuttles, Part IV"|
|Original post date:||2000|
|Previous episode:||"Secret Shuttles, Part III"|
|Next episode:||"The Invisible Enemy"|
Matt and Shane find themselves in the future, the year 2400, where they are met with the future Phoenix-X. The ship is now commanded by a Captain Kugo, who does not allow the two to time-jump back into the past. Matt and Shane are appalled at this and attempt to escape in the timeship, but unfortunately, they only take themselves into another part of the Quadrant. There, they meet with Daniel and Night Seifer, who have rallied a Rebellion against the Section 31 driven Federation. With their help, Matt and Shane are able to bring the timeship back to the year 2375, where Vector 3 is stranded. Unfortunately, because Vector 3 doesn't have the transwarp engine, and there is only enough power for one more jump, they are unable to bring the Vector back. So Daniel leaves Seifer in charge of the Vector for the next two years, ordering him not to alter the timeline. When the timeship returns to the present year of 2377, they meet up with the top-two thirds of the Phoenix-X and recover the bottom third which is now two years older.
- GoyCho admits that Seifer took over Vector 3 on three consecutive occasions to search for the Iso-Star. Two of these occasions would be revealed in the later episodes "Avalon Battlefield, Part I", and "The Nega'Jem, Part II".
- This episode features an alternate future timeline, in which Section 31 was officially recognized in 2384. The organization had enough council members in the Federation to take over and begin launching attacks against the Romulans, the Breen, the Dominion, and the Borg. All were somehow successful by 2400, prompting a Rebellion to uprise against the Federation.
- At the end of this episode, the Commander accepts his new symbiont and therefore his new name, which is Seifer.
- Also at the end, the Phoenix-X drops off Klokian's timeship onto the USS Xena where they request that the Xena take care of the timeship and not let anyone touch it. The timeship would not be seen again until the episode "Phoenix Restoration".
- The "Secret Shuttle" series of episodes would be the only Star Trek: Phoenix-X episodes with subtitles - "Secret Shuttles, Part I": Commencement, "Secret Shuttles, Part II": Furtherence, "Secret Shuttles, Part III": Persistence, and finally "Secret Shuttles, Part IV": Conclusion. This series of episodes would be the only four-parter in the series to date.