|"Secret Shuttles, Part I"|
|Original post date:||2000|
|Next episode:||"Secret Shuttles, Part II"|
A Lieutenant Matt joins the Phoenix-X from the Tech-Team to show the crew the new Paroga-X, a shuttle capable of Transwarp. Meanwhile, the Cardassian ship, Scorpion, brings along Klokian who steals his Timeship back. Two Trill impostors, James and Lex, who were supposedly there to fix the Paroga-X, kidnap and steal Commander Gotens' Gotens symbiont. James places the Gotens symbiont into the Lex host, turning her into Lex Gotens, and takes Lex's previous Seifer symbiont to put into the Commander's Night host - turning him into Night Seifer. At the end of the episode, the Phoenix-X follows the Timeship into the past; the year 2375.
- It is obvious in this episode that the crew of the Phoenix-X aren't working directly for Section 31 at this time, except for that of Lieutenant Wallace. In Season 3 this would change, when the Phoenix-X would begin to have regular contact with Section 31.
- It is revealed that the Iso-star in the episode "Pure Evil" brought the Phoenix-V in from another universe. In the episode "Mirrorlyness!" it will be established that the other universe, of which the Iso-star is connected, is the Mirror Universe.
- This episode marks the beginning of the Commander becoming Seifer. But for the next three episodes, he is referred to as his host name: Night - until the very end of "Secret Shuttles, Part IV" where he begins to accept the Seifer symbiont, his name then changes to Seifer.
- At the end of this episode, the Phoenix-X time-travels back into the episode "Warfare", where "Secret Shuttles, Part II" largely takes place.
- 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.