Published: September 15, 2009 - Updated: August 09, 2014
Rated: PG-13
Genres: Action & Adventure, Alternate Universe, Drama, Mystery & Suspense, Romance
Warnings: None
Challenges: None
Series: The Phantom of Atlantis
Chapters: 50
Completed: Yes
Word count: 164646
Summary: (AU, Part 2 of series) As their second year in Atlantis begins, Elizabeth finds herself drawn ever further into the mystery of the Phantom of Atlantis, while John finds himself constantly torn between what he has become and what he wishes to be...
Rated: PG-13
Genres: Action & Adventure, Alternate Universe, Drama, Mystery & Suspense, Romance
Warnings: None
Challenges: None
Series: The Phantom of Atlantis
Chapters: 50
Completed: Yes
Word count: 164646
Summary: (AU, Part 2 of series) As their second year in Atlantis begins, Elizabeth finds herself drawn ever further into the mystery of the Phantom of Atlantis, while John finds himself constantly torn between what he has become and what he wishes to be...
1. It's a New Dawn by Marcus S Lazarus [Reviews - 4] 
(2302 words)
This marks the second part of my “Phantom of Atlantis” series, an AU take on “Stargate Atlantis” where John Sheppard, instead of being the city’s military commander, is a mysterious masked figure who has been living in Atlantis and fighting the Wraith for almost two decades prior to the expedition’s arrival in the city; reading the first story- “The Phantom of Atlantis”- will be required to understand what’s going on here in greater detail
2: Thanks are due to Manic Penguin, whose story ‘Connections’ inspired some of the plot elements in the upcoming few chapters (All of which are naturally used with her permission)
(2302 words)This marks the second part of my “Phantom of Atlantis” series, an AU take on “Stargate Atlantis” where John Sheppard, instead of being the city’s military commander, is a mysterious masked figure who has been living in Atlantis and fighting the Wraith for almost two decades prior to the expedition’s arrival in the city; reading the first story- “The Phantom of Atlantis”- will be required to understand what’s going on here in greater detail
2: Thanks are due to Manic Penguin, whose story ‘Connections’ inspired some of the plot elements in the upcoming few chapters (All of which are naturally used with her permission)
3. The One I Need, Not the One I Want by Marcus S Lazarus [Reviews - 1] (3012 words)
Not entirely certain about this chapter, but I felt that it had to be written; best to get this issue out of the way before Elizabeth goes back to Atlantis, after all…
(3012 words)Not entirely certain about this chapter, but I felt that it had to be written; best to get this issue out of the way before Elizabeth goes back to Atlantis, after all…
4. Slowly Getting Closer by Marcus S Lazarus [Reviews - 1] (2328 words)
Thanks to everyone who offered their opinions on this chapter; having weighed all possible options, I decided to get straight down to the events of “Intruder” while looking at Sumner’s attitude towards recent events in Atlantis; I figured I could cover his thoughts on the Phantom in transit as easily as I could look at them while he was on Earth
(2328 words)Thanks to everyone who offered their opinions on this chapter; having weighed all possible options, I decided to get straight down to the events of “Intruder” while looking at Sumner’s attitude towards recent events in Atlantis; I figured I could cover his thoughts on the Phantom in transit as easily as I could look at them while he was on Earth
5. Stopping the Virus by Marcus S Lazarus [Reviews - 0] (4243 words)
1: Thanks to Infinite Freedom for suggesting the name of the F-302 pilot I used here
2: Hope you guys like my new resolution for the F-302 crisis; it wasn’t easy to think up, but I like to think I came up with something plausible
1: Thanks to Infinite Freedom for suggesting the name of the F-302 pilot I used here
2: Hope you guys like my new resolution for the F-302 crisis; it wasn’t easy to think up, but I like to think I came up with something plausible
7. All the Pieces of Him by Marcus S Lazarus [Reviews - 1] (3220 words)
AN: The events of this chapter take place just after the events of “Trinity”; the episodes themselves happened in pretty much the same manner as they did in the show- with the obvious exception of Sumner replacing Sheppard-, so there wasn’t much point in rewriting them
(3220 words)AN: The events of this chapter take place just after the events of “Trinity”; the episodes themselves happened in pretty much the same manner as they did in the show- with the obvious exception of Sumner replacing Sheppard-, so there wasn’t much point in rewriting them
8. Getting the Bug Out by Marcus S Lazarus [Reviews - 1] (5606 words)
1: Here we go; “Conversion”, featuring- among other things-, the first Sumner/Phantom match-up…
2: For practicality purposes, this story begins shortly after the check-up we saw in the opening scenes of “Conversion” when Sheppard- or Sumner, in this case- was brought in after being attacked by Ellia only to show no signs of injury; for practical purposes, everything that happened in “Instinct” was basically the same as it was in the original episode, although Sumner was a BIT less inclined to give Ellia the benefit of the doubt than John was
(5606 words)1: Here we go; “Conversion”, featuring- among other things-, the first Sumner/Phantom match-up…
2: For practicality purposes, this story begins shortly after the check-up we saw in the opening scenes of “Conversion” when Sheppard- or Sumner, in this case- was brought in after being attacked by Ellia only to show no signs of injury; for practical purposes, everything that happened in “Instinct” was basically the same as it was in the original episode, although Sumner was a BIT less inclined to give Ellia the benefit of the doubt than John was
9. On to the "Aurora" by Marcus S Lazarus [Reviews - 1] (3523 words)
As promised, my alternate take on “Aurora”, beginning with the group congregating in the control room after McKay announces his discovery of the “Aurora”’s signal
(3523 words)As promised, my alternate take on “Aurora”, beginning with the group congregating in the control room after McKay announces his discovery of the “Aurora”’s signal
10. Failure to Launch by Marcus S Lazarus [Reviews - 1] 
(3499 words)
AN: Sorry about the delay; it was not easy figuring out some of the fine details here
AN 2: Advance warning; I won't be covering the scenes in the simulation, but an explanation of what happened to Sumner while he's in there WILL be provided, I assure you
(3499 words)AN: Sorry about the delay; it was not easy figuring out some of the fine details here
AN 2: Advance warning; I won't be covering the scenes in the simulation, but an explanation of what happened to Sumner while he's in there WILL be provided, I assure you
11. We're All Mad in Our Own Way by Marcus S Lazarus [Reviews - 2] (4571 words)
This chapter will look at some of the events that occurred during the two-part "Lost Boys" and "The Hive", but obviously reference to the precise details of those episodes will be limited due to the majority of the action taking place off-world where John, naturally, cannot go; it's not the most extensive rewrite, but I think it allows for some good insight into John's character at this point in his history
(4571 words)This chapter will look at some of the events that occurred during the two-part "Lost Boys" and "The Hive", but obviously reference to the precise details of those episodes will be limited due to the majority of the action taking place off-world where John, naturally, cannot go; it's not the most extensive rewrite, but I think it allows for some good insight into John's character at this point in his history
12. Questioned Epiphanies by Marcus S Lazarus [Reviews - 1] (2909 words)
1: Not much happens in this chapter- it's essentially just my take on "Epiphany"-, but it does reveal what I think are some interesting hints about John's past and motivations...
(2909 words)1: Not much happens in this chapter- it's essentially just my take on "Epiphany"-, but it does reveal what I think are some interesting hints about John's past and motivations...
14. The Enemy Within by Marcus S Lazarus [Reviews - 1] (4124 words)
AN: Some medical details here regarding dislocated limbs that I'm not that sure about- along with a couple of general details about the chapter as a whole that I'm a bit ambiguous about-, but it was the best thing I could think of for the events depicted that wouldn't cause any serious long-term damage so long as the person responsible knew what they were doing
(4124 words)AN: Some medical details here regarding dislocated limbs that I'm not that sure about- along with a couple of general details about the chapter as a whole that I'm a bit ambiguous about-, but it was the best thing I could think of for the events depicted that wouldn't cause any serious long-term damage so long as the person responsible knew what they were doing
16. The Masks We Wear by Marcus S Lazarus [Reviews - 1] (4183 words)
This begins shortly after the end of the last chapter, with Phoebus having already made contact with Lorne's team and convinced them that she's still Elizabeth; Thalen's role at this point will be pretty much the same as it was originally, but things get more interesting for Phoebus when she's about to take out Lorne's team...
(4183 words)This begins shortly after the end of the last chapter, with Phoebus having already made contact with Lorne's team and convinced them that she's still Elizabeth; Thalen's role at this point will be pretty much the same as it was originally, but things get more interesting for Phoebus when she's about to take out Lorne's team...
17. A Fit of Jealous Rage by Marcus S Lazarus [Reviews - 1] (2150 words)
AN: This takes place after "Coup D'Etat" and a bit before the opening scenes of "Michael", so the Atlantis Expedition have only recently helped Ladon establish himself as leader of the Genii, and are currently experimenting with the retrovirus to transform the Wraith that will come to be known as Michael, although they've only gone so far as to acquire their test subject; Beckett's still testing the virus on live cell samples rather than injecting it into 'Mike' himself
AN 2: It's not my longest chapter, but I think it has its interesting points nevertheless; hope you like it.
(2150 words)AN: This takes place after "Coup D'Etat" and a bit before the opening scenes of "Michael", so the Atlantis Expedition have only recently helped Ladon establish himself as leader of the Genii, and are currently experimenting with the retrovirus to transform the Wraith that will come to be known as Michael, although they've only gone so far as to acquire their test subject; Beckett's still testing the virus on live cell samples rather than injecting it into 'Mike' himself
AN 2: It's not my longest chapter, but I think it has its interesting points nevertheless; hope you like it.
18. Opposites by Marcus S Lazarus [Reviews - 1] (2316 words)
AN: Here we have it; shortly after 'Michael Kenmore' learns the truth about his Wraith origins, and his subsequent confrontation with the Phantom of Atlantis...
(2316 words)AN: Here we have it; shortly after 'Michael Kenmore' learns the truth about his Wraith origins, and his subsequent confrontation with the Phantom of Atlantis...
19. A Trip to Taranis by Marcus S Lazarus [Reviews - 1] (4029 words)
This begins a few days after Michael's escape from Atlantis, leading into the events of Inferno (Albeit with some swiftly-obvious changes...).
(4029 words)This begins a few days after Michael's escape from Atlantis, leading into the events of Inferno (Albeit with some swiftly-obvious changes...).
20. Volcanic Panic by Marcus S Lazarus [Reviews - 1] (3154 words)
This picks up shortly after the last chapter ended; Elizabeth has been briefed on Sumner and McKay's discoveries so far and has come over to talk about the possibility of the Atlantis expedition using the Orion
(3154 words)This picks up shortly after the last chapter ended; Elizabeth has been briefed on Sumner and McKay's discoveries so far and has come over to talk about the possibility of the Atlantis expedition using the Orion
21. Launching the Orion by Marcus S Lazarus [Reviews - 1] (4384 words)
Like the last chapter, this takes place shortly after the previous one; McKay's just been filled in on recent developments and is continuing his analysis of the Orion based on Ronon and Sumner's latest suggestion
(4384 words)Like the last chapter, this takes place shortly after the previous one; McKay's just been filled in on recent developments and is continuing his analysis of the Orion based on Ronon and Sumner's latest suggestion
23. Forging Questionable Alliances by Marcus S Lazarus [Reviews - 1] (3854 words)
I skipped over the conference to discuss Michael's proposal because it wasn't that different from the original version- the only real difference is that Sumner didn't ask Teyla for her thoughts on the plan because, unlike Sheppard, he doesn't particularly care about that issue-, and I felt that subsequent developments after the Wraith arrived on Atlantis would be more interesting to explore anyway (As always, anything you don't see happened pretty much like it did in the show, and I'll try and provide some detail on what happened there where appropriate)
(3854 words)I skipped over the conference to discuss Michael's proposal because it wasn't that different from the original version- the only real difference is that Sumner didn't ask Teyla for her thoughts on the plan because, unlike Sheppard, he doesn't particularly care about that issue-, and I felt that subsequent developments after the Wraith arrived on Atlantis would be more interesting to explore anyway (As always, anything you don't see happened pretty much like it did in the show, and I'll try and provide some detail on what happened there where appropriate)
26. Breaking Into Hives by Marcus S Lazarus [Reviews - 1] (4320 words)
Hope nobody minds about my timing decisions here; later events in the battle against the Hives might be a bit quick, but I think what I've got works in the context of the original episodes
(4320 words)Hope nobody minds about my timing decisions here; later events in the battle against the Hives might be a bit quick, but I think what I've got works in the context of the original episodes
27. Lost Boy Found by Marcus S Lazarus [Reviews - 1] (3708 words)
AN: Hope you like what I've come up with for this chapter- and what's happening in Atlantis will be explored in the next one, I promise-; things are getting a bit more complicated right now, but I feel that this sets the scene for the next chapter or so rather nicely...
(3708 words)AN: Hope you like what I've come up with for this chapter- and what's happening in Atlantis will be explored in the next one, I promise-; things are getting a bit more complicated right now, but I feel that this sets the scene for the next chapter or so rather nicely...
28. The Low Point by Marcus S Lazarus [Reviews - 1] (4430 words)
AN: I had to make a short jump forward for this chapter, but it wasn't that much further than the one we experienced in the episode itself (Even with the Asgard helping Elizabeth and Woolsey return to Atlantis, they can't have been that much faster than the ZPM-enhanced Daedalus, and it still would have taken a few days for the Daedalus crew to get sufficient control of that Wraith ship to take it back to the city)
AN 2: Sorry about the delay in this chapter; real life and writer's block, you know
(4430 words)AN: I had to make a short jump forward for this chapter, but it wasn't that much further than the one we experienced in the episode itself (Even with the Asgard helping Elizabeth and Woolsey return to Atlantis, they can't have been that much faster than the ZPM-enhanced Daedalus, and it still would have taken a few days for the Daedalus crew to get sufficient control of that Wraith ship to take it back to the city)
AN 2: Sorry about the delay in this chapter; real life and writer's block, you know
29. The Fallen Ascended One by Marcus S Lazarus [Reviews - 1] (1003 words)
AN: A quick look at John's perspective on the events of 'Pegasus Project', set towards the end of the episode; hope you like it
(1003 words)AN: A quick look at John's perspective on the events of 'Pegasus Project', set towards the end of the episode; hope you like it
30. Rejection by Marcus S Lazarus [Reviews - 1] (2265 words)
AN: I give you my rewrite of 'Irresistible', which I hope will meet with everyone's approval; it starts promptly, and it probably won't be my longest rewrite, but things are going to become a bit more violent than they were originally...
(2265 words)AN: I give you my rewrite of 'Irresistible', which I hope will meet with everyone's approval; it starts promptly, and it probably won't be my longest rewrite, but things are going to become a bit more violent than they were originally...
31. Breaking the Habit by Marcus S Lazarus [Reviews - 1] (4339 words)
AN: Another individual will get a glimpse at what is hidden under the Phantom's mask in this part of the story, but you'll have to wait until the right moment for a more detailed description; the audience will only get the full answers when Elizabeth does (But I DO have plans for her to learn some useful information soon...)
(4339 words)AN: Another individual will get a glimpse at what is hidden under the Phantom's mask in this part of the story, but you'll have to wait until the right moment for a more detailed description; the audience will only get the full answers when Elizabeth does (But I DO have plans for her to learn some useful information soon...)
32. Loss of a Runner by Marcus S Lazarus [Reviews - 1] (2108 words)
AN: As mentioned, this takes place a couple of weeks after Lucius's departure, exploring the events of 'Sateda'- mainly from the perspective of Atlantis, but with further analysis of how Sumner differs from John as a commander-; hope you like what I have planned
(2108 words)AN: As mentioned, this takes place a couple of weeks after Lucius's departure, exploring the events of 'Sateda'- mainly from the perspective of Atlantis, but with further analysis of how Sumner differs from John as a commander-; hope you like what I have planned
33. Rescuing the Runner by Marcus S Lazarus [Reviews - 1] (3324 words)
AN: A bit of a quicker version than what happened in canon, but I think it works, particularly when the superior strength of the Orion is taken into account.
(3324 words)AN: A bit of a quicker version than what happened in canon, but I think it works, particularly when the superior strength of the Orion is taken into account.
34. Pre-Mission Reflections by Marcus S Lazarus [Reviews - 1] (745 words)
AN: This chapter is relatively short, but it's mainly intended to foreshadow the next one; hope you like it
(745 words)AN: This chapter is relatively short, but it's mainly intended to foreshadow the next one; hope you like it
35. The Real World by Marcus S Lazarus [Reviews - 1] (2962 words)
AN: This begins shortly after the end of "Progeny" before leading into "The Real World"; hope you like it.
As always in these cases, what I don't specifically record happened essentially the same way that it did in the show and will be referenced appropriately, although changes have been made that you'll notice when the time comes; I had a few ideas that I had to include
(2962 words)AN: This begins shortly after the end of "Progeny" before leading into "The Real World"; hope you like it.
As always in these cases, what I don't specifically record happened essentially the same way that it did in the show and will be referenced appropriately, although changes have been made that you'll notice when the time comes; I had a few ideas that I had to include
37. To Him, I Am Beauty Beyond Compare by Marcus S Lazarus [Reviews - 1] (1742 words)
AN: Jumped forward a bit; this chapter's set while McKay's back on Earth for 'McKay and Mrs Miller' (Let's just say I have plans for 'Common Ground' that necessitated it being skipped on this occasion, even without the fact that Sumner would be less open to the idea of an alliance with Todd…)
(1742 words)AN: Jumped forward a bit; this chapter's set while McKay's back on Earth for 'McKay and Mrs Miller' (Let's just say I have plans for 'Common Ground' that necessitated it being skipped on this occasion, even without the fact that Sumner would be less open to the idea of an alliance with Todd…)
38. Same First Name by Marcus S Lazarus [Reviews - 1] (913 words)
AN: Another jump forward, this one exploring Rod's time on Atlantis in 'McKay and Mrs Millar'; all details of our McKay's reunion with his sister and her trip to Atlantis so far are pretty much the same as they were, minus Sheppard slightly flirting with her for obvious reasons
(913 words)AN: Another jump forward, this one exploring Rod's time on Atlantis in 'McKay and Mrs Millar'; all details of our McKay's reunion with his sister and her trip to Atlantis so far are pretty much the same as they were, minus Sheppard slightly flirting with her for obvious reasons
39. What's in a Name? by Marcus S Lazarus [Reviews - 2] (1235 words)
AN: As promised, we've gone straight to the events of "The Return"- nothing really changed much for the rest of Rod's time in Atlantis or during the events of "Phantoms", so I didn't bother rewriting them-, shortly after the expedition has been 'asked' to leave the city…
(1235 words)AN: As promised, we've gone straight to the events of "The Return"- nothing really changed much for the rest of Rod's time in Atlantis or during the events of "Phantoms", so I didn't bother rewriting them-, shortly after the expedition has been 'asked' to leave the city…
40. The Phantom Speaks by Marcus S Lazarus [Reviews - 1] (2699 words)
AN: Alternating between Earth, as Elizabeth carried out her research into her former city's masked protector, and Atlantis, as the aforementioned protector has a 'chat' with its new residents…
(2699 words)AN: Alternating between Earth, as Elizabeth carried out her research into her former city's masked protector, and Atlantis, as the aforementioned protector has a 'chat' with its new residents…
41. City in Peril by Marcus S Lazarus [Reviews - 1] (3671 words)
AN: A predominately Earth-focused chapter this time around, as Elizabeth learns about recent events in Atlantis (Having not been kept as up-to-date as she was in canon because Sumner isn't as interesting in sharing things with her as Sheppard was)…
AN 2: Events in this chapter prompted me to realise an omission I'd made earlier, so I went back and made some changes to 'What's in a Name?' to clarify what happened to the Orion when the Ancients came back; I apologise for any confusion this may have caused.
(3671 words)AN: A predominately Earth-focused chapter this time around, as Elizabeth learns about recent events in Atlantis (Having not been kept as up-to-date as she was in canon because Sumner isn't as interesting in sharing things with her as Sheppard was)…
AN 2: Events in this chapter prompted me to realise an omission I'd made earlier, so I went back and made some changes to 'What's in a Name?' to clarify what happened to the Orion when the Ancients came back; I apologise for any confusion this may have caused.
42. The General and the Phantom by Marcus S Lazarus [Reviews - 1] (2786 words)
AN: To whom it may concern, I'll be focusing more on the Phantom rather than Elizabeth's team at this point in the story- what they'll be doing is fairly similar to what they were doing in canon, such as picking up Niam and returning to Atlantis, so the absence of Sheppard doesn't really have enough impact to make it interesting-, but that will shift when the time is right, I assure you…
(2786 words)AN: To whom it may concern, I'll be focusing more on the Phantom rather than Elizabeth's team at this point in the story- what they'll be doing is fairly similar to what they were doing in canon, such as picking up Niam and returning to Atlantis, so the absence of Sheppard doesn't really have enough impact to make it interesting-, but that will shift when the time is right, I assure you…
44. Under the Mask by Marcus S Lazarus [Reviews - 1] (3828 words)
AN: OK, the votes came in with a general preference for getting straight to the unmasking, so here we are; hope it proves worth it (I've had the actual unmasking written for a while, but the reactions were rather difficult to get right)
(3828 words)AN: OK, the votes came in with a general preference for getting straight to the unmasking, so here we are; hope it proves worth it (I've had the actual unmasking written for a while, but the reactions were rather difficult to get right)
45. History of the Phantom by Marcus S Lazarus [Reviews - 1] (5196 words)
AN: Here we are; the chapter you've all been waiting for, as John reveals how he came to Atlantis in the first place, which I hope will meet with the approval of all concerned parties…
AN 2: In advance, if anyone wonders why the elder Elizabeth here is capable of walking when she barely had the energy to stay awake for more than a few minutes in canon, I'm assuming that, when the stasis chamber was able to complete the revival process on its own as opposed to the process being controlled by the expedition staff who didn't really know what they were doing, it was able to give her an energy boost that would restore her to a condition where she could operate on her own so long as she wasn't pushed too hard, as opposed to her more vulnerable condition in canon
(5196 words)AN: Here we are; the chapter you've all been waiting for, as John reveals how he came to Atlantis in the first place, which I hope will meet with the approval of all concerned parties…
AN 2: In advance, if anyone wonders why the elder Elizabeth here is capable of walking when she barely had the energy to stay awake for more than a few minutes in canon, I'm assuming that, when the stasis chamber was able to complete the revival process on its own as opposed to the process being controlled by the expedition staff who didn't really know what they were doing, it was able to give her an energy boost that would restore her to a condition where she could operate on her own so long as she wasn't pushed too hard, as opposed to her more vulnerable condition in canon
47. The Phantom and the IOA by Marcus S Lazarus [Reviews - 1] (4288 words)
AN: Thanks are due to Elgin, who helped me refine some of my ideas regarding how John can take command of Atlantis given his lack of pre-existing experience with Earth's military, as well as helping me actually write this meeting with the IOA
(4288 words)AN: Thanks are due to Elgin, who helped me refine some of my ideas regarding how John can take command of Atlantis given his lack of pre-existing experience with Earth's military, as well as helping me actually write this meeting with the IOA
48. Reflecting on Earth by Marcus S Lazarus [Reviews - 1] (6906 words)
AN: Once again, thanks to Elgin, who helped me draw up a plan regarding some of the more military-specific details I had to tackle in this chapter, as well as writing some of the training scenes and offering some interesting suggestions for other details that John could deal with now or in the future…
(6906 words)AN: Once again, thanks to Elgin, who helped me draw up a plan regarding some of the more military-specific details I had to tackle in this chapter, as well as writing some of the training scenes and offering some interesting suggestions for other details that John could deal with now or in the future…
50. Return to Atlantis by Marcus S Lazarus [Reviews - 2] (1198 words)
AN: The last chapter of this story, as John assumes his new position in Atlantis; not my longest, but I felt that I stopped at an appropriate point regardless.
(1198 words)AN: The last chapter of this story, as John assumes his new position in Atlantis; not my longest, but I felt that I stopped at an appropriate point regardless.