There are many ways in which this show could have been different.
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- Atlantis was originally planned to supersede SG-1, not run alongside it. Brad Wright and co. planned to end SG-1 after the sixth season finale "Full Circle" and conclude the series with a threatrical film "The Lost City", which in turn would lead into Atlantis. Atlantis would have been discovered under Antarctica, the Goa'uld would have been totally defeated, the Stargate Program would have been made public knowledge and all operations would have been transferred to Atlantis. After SG-1 became a surprise hit after its move to the Sci-Fi Channel, the series was renewed for a seventh season, after which plans for the film were scrapped, and the "the Lost City" was changed into a series finale, which was changed into a season finale after SG-1 was renewed for an eight season. By that time, it became clear SG-1 was not going anywhere, and Atlantis was converted into a spin-off to run alongside SG-1.
- The Replicators were originally planned to be the villains of the series, but after SG-1 was picked up for an eight season, and Atlantis's setting was moved into another galaxy, the Wraith were created to fill their place. The Asurans (Pegasus Replicators) were inspired from this original plan.
- Martouf/Lantash was originally planned to be a major character(s) on Atlantis, but after both characters were killed off (Martouf was originally supposed to survive his ordeal in "Divide and Conquer", but the actor who played the character, JR Bourne, was unavailable for further episodes, so the character was killed off) the plans were axed.
- The original released information for Stargate Atlantis months before the show premiered mentioned that translator devices were among the technology the team would find in Atlantis. This was never seen or mentioned in the series, however, perhaps because it would have caused confusion as to why no such device was ever necessary in SG-1.
- Some early information suggested that Atlantis itself was sentient with the holo room projecting a persona for the team to interact with. This was likely dropped because it was too similar to Andromeda, which was airing at the time.
- Joseph Mallozzi, showrunner for the series, pitched a number of detailed episode ideas that never got off the ground:
- During Season 2, he pitched an idea about the Atlantis expedition running into a little girl being chased by a frenzied mob on a planet. They rescue the girl, bring her back to Atlantis, all is well until mysterious accidents and happenings begin occuring to anyone who crosses the little girl in the wrong way. The team investigates her home planet, and discovers the same happened there, hence the mob chasing her. They then discover an Ancient lab with a long dead Ancient corpse within a statis pod, and discover that this Ancient has transferred his consciousness and powers into the little girl, so they go back to Atlantis to stop her. No one else on the show liked the idea, so it was axed.
- During Season 3, he pitched a story about a civilization called the Drazia, humans who like the Genii have carefully hidden their advanced technology from the Wraith, and have even discovered a way to prevent being culled. Turns out their method involves transferring their consciousness into old, decaying bodies, leaving their young, healthier bodies to be culled, and then when all is over, they prey on visitors to their planet, stealing their bodies. It was probably rejected for how weird it was.
- Another story pitched during Season 3 involved Sheppards team returning from a routine mission to find the entire crew of Atlantis turned into Wraith-Human hybrids, and discovering that, according to Atlantis, they've been gone for several months. They learn that the Wraith Michael is behind this, using an modified aerosolized version of the Beckett retrovirus to turn the entire crew into Wraith-Human hybrids to do his bidding , and that he is planning an invasion of Earth. The story was apparently rejected because of the time travel angle, however the concept of Michael creating Wraith-Human hybrids did eventually appear in Seasons 4 and 5, and a very similar plot of Michael turning the crew of Atlantis into hybrids was apparently planned for season 6.
- During Season 4, a story was pitched about a joint operation between Atlantis and the Genii infiltrating a Wraith compound, with the Atlantis team suspecting that the Genii are not totally forthcoming about the operation, eventually discovering they weren't and why: the compund is a Wraith nursery housing 12 would-be queens. The Atlantis team would then have to decided whether to murder the children, and thereby crippling and even possibly destroying the Wraith, or sparing the children who would inevitably grow up to terrorize and kill millions of people. It's a plot that would have made Star Trek: Deep Space Nine (and a lot of modern day television for that matter) proud. The story was rejected because no matter what option was taken, the Atlantis team would not come out as heroes. Moral exploration and ambiguity was a no-no on Atlantis apparently.
- Various other episode ideas, both throughout its run and for the planned sixth season, were considered:
- An episode involving Samantha Carter facing a court martial and dismissal, described as a take on Akira Kurosawa's "Rashomon" was pitched in Season 4, but was rejected. Interestingly, it's similar to a pitch Ronald D Moore made for Star Trek: Voyager involving Captain Janeway in a similar situation.
- The sixth season premiere would have involved Atlantis having to get back to the Pegasus Galaxy after an auto-destruct feature that the Ancients left to activate if the city left Pegasus is turned on, by using the Wormhole Drive featured in "Enemy At The Gates" which would have accidentally sent them to another galaxy. After the series was cancelled, the season premiere was to be re-worked as either a straight-to-DVD or TV movie called "Stargate Extinction" but it was shelved after MGM's bankruptcy and Stargate Universe's cancellation.
- An episode was planned involving the Daedalus finding a derelict ship with children in stasis, who upon being revived ask the Daedalus to take them to their homeworld. A mysterious ship soon appears afterwards and constantly attacks the Daedalus, with the crew eventually wondering if the children are behind this.
- An episode involving a witch (yes, a witch) cursing Shepard for being an asshole to her, which causes him to have a streak of bad luck, was planned but rejected.
- An episode was planned involving the Atlantis team running afoul of an alien species, who ends up using some sort of temporal effect that sends them several months into the future, where they were presumed missing and replaced by a new team. The team would have to find a way to adjust to this, with the alien species eventually coming to pay Atlantis a visit.
- An episode involving Mc Kay experimenting with a time traveling jumper (presumably Janus's) and accidentally sending the team backwards, forwards (to a future where the Wraith control Atlantis) and back to the present over and over again with constant changes to the timeline was planned but shelved because it was considered too confusing.
- The Vanir, the rouge Asgard from "First Contact" and "The Lost Tribe" were slated to return as a serious threat.
- The unnamed aliens from "The Daedalus Variations" were considered for a re-appearance. This plot would eventually get used in the American Mythology Productions comics set after the series.
- Joseph Mallozzi mentioned in an AMA that a scenario involving Goa'ulds taking over Wraith was briefly considered, but rejected because the writing staff didn't "want to open that can of worms".
- Joseph Mallozzi revealed that "following SGAs fourth season, there had even been some talk of having Daniel [Jackson] join the Atlantis crew for its fifth season, an idea we unfortunately had to abandon for financial reasons." He did however guest star in "First Contact" and "The Lost Tribe".
- According to Joe Flannigan, after the series was cancelled and Stargate Universe began airing, he, alongside some investors, approached MGM to buy the franchise to continue Stargate Atlantis. MGM was not willing to sell, but agreed to lease the franchise to him, with sets in Europe set up to start filming episodes again. MGM then went bankrupt however, and was bought by Spyglass, who prompty cancelled the faltering Stargate Universe and cancelled any plans to lease the franchise to Flannigan, preferring instead to approach Roland Emmerich about a reboot film trilogy, totally disregarding the entire television franchise, which ultimately didn't happen. Flannigan also claims that the purportedly planned Atlantis film "Stargate: Extinction" never had great sincerity behind it, and that the announcement of it was a "trial balloon" to appease the fanbase who felt insulted by SGU and its advertising ("we're going for a younger, sexier audience", for example).