Published: August 09, 2014 - Updated: February 03, 2019
Rated: PG-13
Genres: Action & Adventure, Alternate Universe, Angst, Drama, General, Hurt/Comfort, Introspective, Mystery & Suspense, Romance
Warnings: None
Challenges: None
Series: The Phantom of Atlantis
Chapters: 26
Completed: No
Word count: 73569
Summary: With his position in Atlantis now official, John must overcome his own perception of himself as old foes assume a new approach and his relationship with Elizabeth develops further
Rated: PG-13
Genres: Action & Adventure, Alternate Universe, Angst, Drama, General, Hurt/Comfort, Introspective, Mystery & Suspense, Romance
Warnings: None
Challenges: None
Series: The Phantom of Atlantis
Chapters: 26
Completed: No
Word count: 73569
Summary: With his position in Atlantis now official, John must overcome his own perception of himself as old foes assume a new approach and his relationship with Elizabeth develops further
Story Notes:
Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval
Feedback: Always appreciated, trust me
AN: The third part in my 'Phantom of Atlantis' trilogy (Reading the first two stories in the series is highly recommended to ensure that you understand what's going on); for those returning fans, this take place about a month after the conclusion of 'Mystery of the Phantom', and as currently planned will cover the remaining key storylines in 'Atlantis', with some obvious and significant differences…
Feedback: Always appreciated, trust me
AN: The third part in my 'Phantom of Atlantis' trilogy (Reading the first two stories in the series is highly recommended to ensure that you understand what's going on); for those returning fans, this take place about a month after the conclusion of 'Mystery of the Phantom', and as currently planned will cover the remaining key storylines in 'Atlantis', with some obvious and significant differences…
1. Out of the Mask by Marcus S Lazarus [Reviews - 2] 



(1749 words)
AN: Thanks are due to Elgin, who helped me refine a few details regarding the consequences of John's new role





AN: Thanks are due to Elgin, who helped me refine a few details regarding the consequences of John's new role
2. John Sheppard's First Night Out by Marcus S Lazarus [Reviews - 1] 



(2693 words)
AN: This chapter proved tricky at times, but I hope it was worth it; we're coming up to my interpretation of one of my favourite episodes of 'Atlantis'…





AN: This chapter proved tricky at times, but I hope it was worth it; we're coming up to my interpretation of one of my favourite episodes of 'Atlantis'…
6. The Digital Ark by Marcus S Lazarus [Reviews - 1] 



(4451 words)
AN: Another shorter rewrite, but that's the way things go; I skimmed over a couple of details, but I hope you'll like the result anyway.





AN: Another shorter rewrite, but that's the way things go; I skimmed over a couple of details, but I hope you'll like the result anyway.
9. Exploding Tumours by Marcus S Lazarus [Reviews - 1] 



(3687 words)
AN: And here we are with the events of 'Sunday'; hope you enjoy the results





AN: And here we are with the events of 'Sunday'; hope you enjoy the results
14. Assault on Atlantis by Marcus S Lazarus [Reviews - 1] 



(3523 words)
AN: I apologise in advance that this chapter doesn't end this episode, but it felt like it would be too long if I included Atlantis taking off as well given my other plans for these events; hope you like the results anyway





AN: I apologise in advance that this chapter doesn't end this episode, but it felt like it would be too long if I included Atlantis taking off as well given my other plans for these events; hope you like the results anyway
16. Confrontation on Asuras by Marcus S Lazarus [Reviews - 2] 



(4828 words)
AN: And this chapter, that moment that made so many fans unhappy…
Hope you enjoy my own spin on it.





AN: And this chapter, that moment that made so many fans unhappy…
Hope you enjoy my own spin on it.
18. Darkening Dreams by Marcus S Lazarus [Reviews - 1] 



(1570 words)
AN: For the record, I decided not to look at the events of 'Reunion', considering that the key details wouldn't be altered whether Sam or Elizabeth was in charge of Atlantis- apart from Elizabeth being maybe slightly more explicitly upset about having to reject Ronon's initial request for his old friends to come to the city, as she knew him better than Sam would have at that time- but I also felt that 'Doppelganger' had more obvious plot potential considering the psychological issues it would force John to confront





AN: For the record, I decided not to look at the events of 'Reunion', considering that the key details wouldn't be altered whether Sam or Elizabeth was in charge of Atlantis- apart from Elizabeth being maybe slightly more explicitly upset about having to reject Ronon's initial request for his old friends to come to the city, as she knew him better than Sam would have at that time- but I also felt that 'Doppelganger' had more obvious plot potential considering the psychological issues it would force John to confront
19. The Unscarred Doppelganger by Marcus S Lazarus [Reviews - 1] 



(2626 words)
AN: Hope this chapter works; I thought about going over the dreams in more detail at first, but decided it would be more interesting to cut to the moment when John realises who/what he's up against





AN: Hope this chapter works; I thought about going over the dreams in more detail at first, but decided it would be more interesting to cut to the moment when John realises who/what he's up against
21. Meeting the Travellers by Marcus S Lazarus [Reviews - 1] 



(3229 words)
AN: Reference is made in this chapter to a group known as 'the Pack', who appear in the Stargate SG-1 novel 'Relativity'; if you're a fan of the series, I can recommend that book in particular, as it features such gems as the return of a devastating old enemy, Kinsey getting taken down a few pegs as he tries to make a political breakthrough, and a time-travel situation that sees a certain member of SG-1 actually meeting themselves…





AN: Reference is made in this chapter to a group known as 'the Pack', who appear in the Stargate SG-1 novel 'Relativity'; if you're a fan of the series, I can recommend that book in particular, as it features such gems as the return of a devastating old enemy, Kinsey getting taken down a few pegs as he tries to make a political breakthrough, and a time-travel situation that sees a certain member of SG-1 actually meeting themselves…
22. The Treaty with the Travellers by Marcus S Lazarus [Reviews - 1] 



(1938 words)
AN: This part of the storyline ended up being shorter than I'd expected it would, but I hope everyone liked the result anyway





AN: This part of the storyline ended up being shorter than I'd expected it would, but I hope everyone liked the result anyway
23. The Other Phantom by Marcus S Lazarus [Reviews - 1] 



(1630 words)
AN: Another episode 'jump', but I felt that it was appropriate. John would still be reduced to an amnesic state in "Tabula Rasa" as he didn't arrive in the Pegasus Galaxy at an age when he'd have been young enough to gain an immunity to Kirsan fever (and he was obviously spending time in isolation when he arrived, so would have been unlikely to be in a position to be infected with it anyway), so his presence wouldn't change much about the episode apart from some people freaking out about his face. That said, this chapter will begin during the events of "The Missing" while Teyla and Jennifer are away, and feature a VERY significant development in my storyline that would have never happened in the show for reasons that will soon become obvious…





AN: Another episode 'jump', but I felt that it was appropriate. John would still be reduced to an amnesic state in "Tabula Rasa" as he didn't arrive in the Pegasus Galaxy at an age when he'd have been young enough to gain an immunity to Kirsan fever (and he was obviously spending time in isolation when he arrived, so would have been unlikely to be in a position to be infected with it anyway), so his presence wouldn't change much about the episode apart from some people freaking out about his face. That said, this chapter will begin during the events of "The Missing" while Teyla and Jennifer are away, and feature a VERY significant development in my storyline that would have never happened in the show for reasons that will soon become obvious…
25. Nice Job Breaking It, Atlantis by Marcus S Lazarus [Reviews - 1] 



(2382 words)
AN: As we begin my take on "The Seer", I apologise in advance for skipping some of Davos's scenes, but they were basically the same as in the show, considering McKay's scepticism on the matter of his visions, so I thought it best to get to the more interesting elements





AN: As we begin my take on "The Seer", I apologise in advance for skipping some of Davos's scenes, but they were basically the same as in the show, considering McKay's scepticism on the matter of his visions, so I thought it best to get to the more interesting elements
26. Debate with Woolsey by Marcus S Lazarus [Reviews - 1] 



(1641 words)
AN: Apologies, but after this chapter, this story's going on hiatus for a bit; I want to work on a couple of other projects on other sites, so as I've been feeling a bit less inspired by certain fics lately, this is one of the storylines I'm putting aside to let me focus on my new ideas. Be assured that I have a fairly clear storyline planned out for these other projects and will get back to this as soon as is feasible





AN: Apologies, but after this chapter, this story's going on hiatus for a bit; I want to work on a couple of other projects on other sites, so as I've been feeling a bit less inspired by certain fics lately, this is one of the storylines I'm putting aside to let me focus on my new ideas. Be assured that I have a fairly clear storyline planned out for these other projects and will get back to this as soon as is feasible