Published: September 15, 2009 - Updated: July 05, 2010
Rated: PG-13
Genres: Action & Adventure, Alternate Universe, Drama, Mystery & Suspense, Romance
Warnings: None
Challenges: None
Series: The Phantom of Atlantis
Chapters: 15
Completed: No
Word count: 53168
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: 15
Completed: No
Word count: 53168
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] (4156 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
(4156 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