|"Secret Shuttles, Part II"|
|Original post date:||2000|
|Previous episode:||"Secret Shuttles, Part I"|
|Next episode:||"Secret Shuttles, Part III"|
Klokian steals his Timeship and initiates a time-jump as Captain Daniel tractor-beams the Timeship during this jump from within the Paroga-X. The Phoenix-X decides to jump Transwarp, right through both the Paroga-X and the Timeship as the time-jump is happening - sending all three vessels into the past; to the year 2375. Upon entrance, Daniel and the Paroga-X are disoriented until running into a Section 31 ship; here Daniel is able to confirm that Wallace really is working for Section 31. Upon entrance, Klokian takes his Timeship to the 2375 Phoenix-X, where he saves Gul Meloneus by beaming the Gul onto the Timeship a second before the Gul's ship is destroyed. Upon entrance, the Phoenix-X decides to drop Transwarp a few lightyears away, where Night Seifer steals Vector 3 to follow the escaping James Gotens and Lex Gotens into the other universe through the Iso-star.
- This episode takes place within the episode "Warfare"
- Since by this time, Sloan is killed in Star Trek: Deep Space 9 continuity, Sloan's brother, Floan, is used.
- In most early Season 1 episodes, the Phoenix-X was consistently mis-spelled as "Pheonix-X" until the end of the episode "Warfare". Since this goes back to that episode, all references, in this episode, to the (past) 2375 Phoenix-X are intentionally mis-spelled "Pheonix-X" and all references to the 2377 Phoenix-X are intentionally correctly-spelled "Phoenix-X".
- The star in the Essex system goes nova in this 2375 timeframe, due to the 2375 Phoenix-X's Slipstream torpedo. This is consistent with the events in "Warfare".
- At the end of the episode, Vector 3 enters the other universe - which is referred to as the nega-universe within the episode. In the Season 3 episode "Mirrorlyness!" it will be established that this is the Mirror Universe.
- The end of the episode marks the last time Vector 3 would be attached to the Phoenix-X until the end of the year and a half long Vector 3 time-loop. The Vector 3 time-loop would later be revisited in the Season 2 episode "The Nega'Jem, Part II," and the Season 3 episode "Avalon Battlefield, Part I," but conclude at the end of the "Secret Shuttle"'s four-parter "Secret Shuttles, Part IV".
- At the end of the episode, the crew onboard Vector 3 are not only now back in time to 2375, but also in the Mirror Universe of that year.
- This episode also illustrates Night Seifer's obsession with getting the Gotens symbiont back. The obsession would later be revisited in "Avalon Battlefield, Part I".
- 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.