The Lost Season of Stargate Atlantis

With five seasons and exactly 100 episodes to its name, Stargate Atlantis solidified itself as one of the great sci-fi shows of its decade when it went off the air in 2009.

The show premiered in July 2004 (yep, nearly 20 years ago!) and starred Joe Flanigan as Major John Sheppard, Torri Higginson as civilian leader Dr. Elizabeth Weir, David Hewlett as surly scientist Dr. Rodney McKay, Rachel Luttrell as alien queen Teyla Emmagan, and Rainbow Sun Francks as the young Lt. Aiden Ford.

After Brad Wright and Robert C. Cooper created the series, in the fourth and fifth season executive producers Joseph Mallozzi and Paul Mullie took over day-to-day showrunning duties. By the time fifth and final season arrived Jason Momoa was on the cast as Specialist Ronon Dex, and Robert Picardo’s Richard Woolsey was in charge of Earth’s expedition to the city of the Ancients in the Pegasus Galaxy. Several promotions, alliances, and vanquished foes later and Atlantis concluded its fifth and final season on January 9, 2009.

And then, there was Season Six. With new antagonists introduced in the fifth season’s final stretch of episodes, the writers had every intention of continuing the show. The team saved Earth from a Wraith super-hive and ended up parking Atlantis itself outside San Francisco Bay … but the series was never supposed to end there.

So what was next? Thanks to Joseph Mallozzi, we have a surprisingly thorough accounting of the stories that could have been told in a sixth season … had Stargate Atlantis not been cancelled.

It all starts with this photo, which Mallozzi snapped in the writer’s room on his way out the door:

Joseph Mallozzi / Reddit

The writing team had begun brainstorming some ideas for the next season’s 20 episodes — some that had been set up in the fifth season, characters worth revisiting, and pitches that hadn’t made the cut but might be reworked.

But the show was cancelled, with MGM instead planning to turn Atlantis into an ongoing series of DVD movies (which, sadly, never materialized). Now it’s been 15 years since SGA went off the air, and Mallozzi (who went on to co-create Dark Matter for Syfy Channel) is revisiting the show’s “lost” episodes (which he first revealed in 2008, after the cancellation). In a newly updated post across social media Mallozzi has summarized the team’s original plans for Season Six, fleshing out some of the ideas a bit further and also integrating the scene he wrote for 2019’s Atlantis cast reunion and table reading at San Diego Comic-Con — featuring the return of Torri Higginson’s Elizabeth Weir.

Whether this ever would have actually happened in a sixth season of the show … well, if it’s an ex post facto fantasy we are here for it! I read all of this as something of a producer’s wishlist, which certainly would have undergone changes in the normal course of television production. But it’s an amazingly detailed look at what might have been.

Here is the full season run-down, with a bit of commentary on what might have been. Be sure to read Mallozzi’s full breakdown of every episode pitch on Twitter or Reddit! You can also watch the video above for the full, episode-by-episode breakdown.


Episodes #601 – #602

In the months since Season Five’s fade-to-black Atlantis has been relocated to the surface of Earth’s Moon, operating as a new base (while the I.O.A. and various Earth interests debate what to do with the city). An emergency security measure forces the team to fly back to the Pegasus Galaxy, but along the way they are stranded in the Triangulum Galaxy — where they are stunned to find a human civilization who appear to be their own descendants (an idea that would later be reused for the SGU episode “Common Descent”).

The opening two-parter would have featured time travel, and a future version of Todd the Wraith (Christopher Heyerdahl) as the chief antagonist. Only with help from present-day Todd can the Atlantis team “turn the tables on the enemy and resume their journey to the Pegasus Galaxy.” “Now What?” (or whatever the final title would have been) eventually became the Atlantis movie Stargate: Extinction, which was fully scripted but never produced.


Episode #603

Sheppard’s team on board the Daedalus comes across a seemingly derelict ship, and on board they find a group of children in stasis. The kids explain their ship was en route to be reunited with their parents on a new colony (making them one of Pegasus’ rare, space-faring civilizations). Of course our heroes agree to help them reach their destination — but soon another mysterious ship appears and opens fire on Daedalus! These kids are definitely not all that they appear to be, and the crew has to figure out what is really going on while playing a deadly game of cat and mouse with their pursuer.


Episode #604

The great Carl Binder had penned Season Five’s “Ghost in the Machine,” hoping to bring back the Replicator version of Elizabeth Weir. (The role was recast with “Fran” actress Michelle Morgan after Higginson turned it down.) This version of Weir was left drifting in space, along with her fellow Replicators who had been seeking ascension.

In Season Six, we might have seen this group return for another story … though this one sounds like more of a placeholder than a fully realized story pitch. Binder was also great at ghost stories (such as “Echoes”), and Mallozzi said that the team assumed he would return from hiatus with either a ghost story or a Replicator story ready to go. “Carl Binder was the king of ghost and Replicator stories,” Mallozzi said. “No doubt he would have written one for the show’s sixth season. And it would have been brilliant.”


Episode #605

Writer Martin Gero loved looking for ways to tell unique stories that subverted the Stargate formula. For years he wanted to write an episode all about the team’s day off, when they aren’t on a mission or facing a crisis. (That eventually turned into “Sunday,” an episode where a day off in Atlantis very much becomes about a sudden crisis.)

This slot in the sixth season was intend for another off-beat idea: “‘Classic Stargate’ was an idea Martin Gero pitched, a story that would take place in the early years of the Atlantis expedition, a flashback to an adventure we had never been privy to,” Mallozzi says. Could we have seen Rainbow Sun Francks back as an optimistic young Lt. Ford? Maybe a good old fashioned Z.P.M. hunt? It’s an interesting idea to tell a Season One story during Season Six — but this one would probably need some sort of connection to the present day to make it past the pitch stage.


Episode #606

Often the brainstorming session for next season begins with pitches that are already on the table but didn’t make the cut. That was the case here, with a fourth-season episode intended for Amanda Tapping’s Colonel Samantha Carter. The idea was deemed good enough for the writers to hold on to in Season Five, and then to push again to Season Six … though with Tapping now off starring in her own show (Syfy’s Sanctuary) this story might have been given to another character.

“Carter Rashomon” was envisioned as Stargate’s take on Rashomon, the classic 1950 film by Akira Kurosawa that depicts the same event multiple times from the radically different viewpoints of various witnesses. Here an off-world op has gone so badly that Colonel Carter is facing a possible court martial. The episode follows the investigation, and through flashbacks the audience is shown three different versions of the events that transpired. What really happened? Whose account should be believed?

This pitch would have made a great vehicle for the base’s new commander, Richard Woolsey (Robert Picardo). While he isn’t in the military and so couldn’t be court-martialed, it would certainly fit with Woolsey’s storyline to see the I.O.A. and Homeworld Command show up to conduct the same sort of inquiry to which Woolsey himself used to subject other people. Guest appearances by Tamlyn Tomita (Shen Xiaoyi) and Richard Dean Anderson (Jack O’Neill), anyone?


Episode #607

Stargate SG-1 had its “lower decks” episode with “The Other Guys,” and the Atlantis writing team was looking to do the same here. While this one doesn’t seem to have been a fully fleshed-out story idea, Mallozzi says that “Carl Binder wanted to do a story told from the POV of a red shirt, one of those ubiquitous no-names we lose over the course of an op who is mourned then quickly forgotten in the episode tag when the team is yukking it up in the cafeteria.”

Binder suggested a story that would see an ordinary member of the expedition not killed in the line of duty but rather captured. Because we don’t leave our people behind, Sheppard and his team mount a rescue operation.


Episode #608

A Sheppard-centric episode “would have seen John racing against time to find out how he was infected with a deadly toxin and, ultimately, who was responsible and why.” Inspired by the 1950 noir thriller D.O.A., the episode would have put the character (and the audience) through the ringer as they spend the entire hour believing that John Sheppard is more or less a goner. But of course, as John and his team race to find out who killed him and why, they would no doubt find an antidote along the way.


Episode #609

On the run from an alien race, Sheppard’s team ends up caught up in a temporal effect of some sort (is it an accident? is it a weapon?) that sends them six months into the future. When the team returns to Atlantis they learn that they were given up for dead, and replaced with a new lead reconnaissance unit.

This pitch came from Atlantis co-creator Brad Wright, with a time-travel twist reminiscent of 2008’s Stargate: Continuum: What happens when our heroes can’t undo what has happened to them, and are forced to settle into daily life in their new reality? Sheppard and the team try to move forward (including working alongside their replacements, whom Woolsey isn’t about to kick to the curb because McKay and company are back). But then … the alien race that was pursuing them pays Atlantis a visit.


EpisodeS #610 – #611

From “The Storm” to “The Lost Tribe,” Stargate Atlantis knew how to go big for its mid-season double episodes. It was a chance to advance the show’s major story arcs, book a big guest star, and spend money on those epic visual effects. Season Six would have been no different, this time with a story that pitted Sheppard’s team against their own people. (This story was left a little vague in Mallozzi’s original post, but in the years since he seems to have settled on what he wanted to do with these pivotal episodes.)

The untitled two-parter would have seen the return of Connor Trinneer as the Wraith hybrid, Michael — who fans (and the actor himself) long suspected did not really die when he fell from the central tower at the end of Season Five’s “The Prodigal.” Michael is alive and (relatively) well, it turns out, and now he is out for revenge. As the story opens the team returns home after a mission, only to find Atlantis teeming with Wraith hybrids — servants of Michael who have eerily familiar faces!

Michael has used a biological weapon to transform Atlantis’s personnel into hybrids, and the team soon find themselves on the run not only from Michael but from their friends. Can they thwart the enemy’s nefarious plan and rescue their people?


Episode #612

If ever there was an intriguing title that didn’t have a story yet, it’s “Hamster Ball.” This idea came from the mental picture of our team trapped inside giant, spherical containment vessels. Mallozzi adds: “Compounding the problem is the fact that they are trapped in a small chamber, in direct line of the Stargate, meaning the next time the gate kawooshes they risk total annihilation. How do they get trapped? How do they get out? And, most importantly, what the hell else happens in this episode? You’ll have to ask writer Alan McCullough.”

Trapping our heroes with a ticking clock is an idea as old as television. Yeah, I would have been all-in on a story that sees a frustrated Hamster Rodney, shall we say, “spinning his wheels.”


Episode #613

Another time-travel dilemma stems from Atlantis’s discovery of a Puddle Jumper capable of traveling through time (like the one SG-1 found in the Milky Way). Of course McKay wants to experiment with a technology that is beyond his understanding, and disaster ensues: duplicate versions of the team are sent both backwards and forwards in time.

As this mind-bending hour unfolds, one version of our heroes find themselves five years in the past, where they try to find the Jumper again to undo the error without altering their own history. Five years into our future, a second team finds Atlantis under siege by those ruthless aliens we met in a parallel universe in “The Daedalus Variations”! This Sheppard and company go looking for the Jumper to try and warn their past selves about what’s coming. And finally, in the present day Dr. McKay continues to tweak his experiment to get it just right. Events in each time period affect what is happening in the others, leading all three timelines to an exciting and mind-bending climax.


Episode #614

Another “Sheppard in peril” story would have seen John apparently put under a curse by an eccentric villager while visiting an alien community. The team laughs it off, but after returning home Sheppard starts to experience an increasingly unusual string of bad luck. Says Mallozzi: “Shep whumpers rejoice!”

Ultimately this story was shelved because it would have painted the show’s leading man in an overly comical and potentially unheroic light. Had it made the cut in Season Six, “Hexed” likely would have needed some reworking. Maybe it’s McKay, the man of science and butt of many a joke, who gets cursed by the alien witchdoctor?


Episode #615

“Entropy” originated in Season Five when producer Paul Mullie pitched a story in which the interdimensional bridge that Rodney and his sister Jeannie had engineered (“McKay and Mrs. Miller”) has unforeseen ramifications for the city of Atlantis. The bridge idea ended up used for Season Five’s “Brain Storm” (having been reproduced on Earth), so Mallozzi reworked the idea for this episode using a mishap with a Zero Point Module.

The Z.P.M., of course, is the Ancient’s power source that draws energy from a contained pocket of subspace time. Should something go catastrophically wrong with what is essentially a pocket universe in a bottle, the story potential is limitless. “I reimagined a version where a mishap with a Z.P.M. triggers a subspace burst that disperses time fractals throughout Atlantis,” Mallozzi says. “And within these varying shards of warped spacetime, the rules of physics no longer apply.”

As a Star Trek: Voyager fan this sounds a bit like “Shattered,” a fantastic episode in which Chakotay has to move through different sections of the ship that have been split into various periods in its timeline. Or Farscape fans will think of “Through the Looking Glass,” another mind-bender where a starburst accident leaves Moya split into multiple dimensions. A Stargate take on this would have been amazing!


Episode #616

As the new season enters its final stretch it’s time to check in on our good frienemy Todd. The cunning Wraith usually manages to come out on top, forming an alliance with Atlantis to defeat the Replicators (and steal a few Z.P.M.s while he’s at it) in Season Four, and using Teyla to help him dispatch a rival queen so that he can assume command of her armies in Season Five (“The Queen”). But in this lost episode, it seems that the enemies Todd has made along the way finally catch up with him.

Now Todd has been captured by his rivals, and when the Atlantis team learns of his fate they decide it is in their best interests to try and mount a rescue mission. (Better the devil you know in charge of a huge alliance of Wraith hive ships.) To pull off this risky gambit Teyla agrees to go under the knife and be surgically altered once again. Resuming her role as Todd’s Wraith queen, “Teyla leads the team aboard a hive ship in order to track down and rescue their unlikely ally.”

Todd is such a great character that we’d certainly expect him to survive this one. And now he would owe Atlantis one whopper of a favor.


Episode #617

An unknown assailant has been attacking Atlantis recon teams on different worlds, and Colonel Sheppard decides it’s time for his team to track them down and stop them once and for all. But the team find themselves under attack by a Puddle Jumper of all things. Now on the run on an alien world, the team realized that the one who is pursuing them seems to be able to predict their every move.

“Payback” could have been the writers’ long-awaited chance to bring back Aiden Ford (played by Rainbow Sun Francks), an original member of their expedition who became addicted to a Wraith enzyme that gave him super-human strength (and messed up his head). When last we saw him back in Season Two, the rogue Ford had recruited his own team to go on the offensive against the Wraith. But an ill-advised mission to infiltrate a hive ship left Ford presumed dead (“The Hive”).

When he returns it’s clear that Ford holds his former team responsible. He’s recruited a new team of mercenaries, surprisingly armed with Ancient tech. Where is Ford getting this stuff? Mallozzi teases: “Our heroes must find a way to turn the tables on their former friend — and, ultimately, find out the surprising source of his all-too familiar resources.”


Episode #618

Mallozzi has lambasted this vague title enough that we know it’s just a placeholder, originally put on the list because the writers thought it was funny. But 15 years later Mallozzi has a great idea for the lost season’s eighteenth episode. Ford has been captured and is now in a holding cell in Atlantis, and the team sets out to locate the source of his black-market Ancient tech. The most likely candidate? Another Ancient city ship, which they first discovered back in the second-season episode “The Tower.”

The city was last seen in the hands of the planet’s local inhabitants, who traded Puddle Jumpers and drones with Atlantis for medical supplies and other support. But when the team arrives to investigate in this lost episode, they find that the city has fallen into the hands of a rogue group of Genii soldiers — under the leadership of none other than Acastus Kolya himself (Robert Davi). Mallozzi hoped to show how this great villain and foil for Colonel Sheppard had in fact survived their shoot-out (back in Season Three’s “Irresponsible”) using his own personal shield emitter, and since then Kolya has been lying low and consolidating his power — and his access to Ancient technology. Kolya once coveted the power of Atlantis, and now it seems he has an Ancient city all his own.

Ultimately the team is unable to defeat the Genii and retake the city for its original inhabitants, and they are forced to retreat — “but not before they obtain a crucial piece of information: the mirror location of the Ancient Z.P.M. factory hidden on Atlantis.” Finding where the Ancients secretly manufactured this important power source is a game-changer for the show, and would have answered a long-standing question from fans.


Episode #619

The cast reunion and table reading at San Diego Comic-Con in 2019 gave Joseph Mallozzi the opportunity to write dialogue for these characters once again — and it was so much fun that he even posted the script pages for all to read. It was an original scene that let the actors play off each other in front of a crowd of fans … but it also contained one giant story beat that Mallozzi wanted to work into the show itself: the return of Torri Higginson’s Elizabeth Weir.

The events of “Ghost in the Machine” notwithstanding, in Mallozzi’s pitch the team would have found the original (biological) Elizabeth alive and well, kept on ice since her capture by the Asurans. The version we saw following her capture in “Lifeline” was evidently a Replicator copy of her consciousness, who believed that she was the real Elizabeth whose body had been entirely transformed by the nanites in her system. The penultimate episode of Season Six would see the team finding Dr. Weir, after Atlantis’s hidden Z.P.M. chamber points them to other such secret storehouses throughout the Pegasus Galaxy.

With Elizabeth’s help the team searches for a powerful weapon left behind by the Replicators, which they built to destroy Atlantis. Our heroes hope to use it against Kolya’s Ancient city ship before he can use the city to wreak havoc … but they arrive too late. Kolya’s ship lifts off from the surface of its home planet, headed for Atlantis.

Whether this was just fan service or might have actually come to pass on the show, it’s a great idea that in my mind would have righted a couple of wrongs from the show’s past. Elizabeth, Carson, Ford, Kolya … the show had a tendency to kill off important characters in less-than-satisfying ways.


Episode #620

The newly expanded plot for the finale of Atlantis‘s lost season continues where the previous episode left off, as the team returns home with a warning that the rogue Genii are bringing Atlantis’s sister city to attack. As Mallozzi tells it today, the episode would begin with a series of character moments as the expedition recalls all off-world teams and makes ready for war. Then they launch Atlantis into planetary orbit, ready to meet Kolya and the Genii on an even footing.

If you want to know the rest of the story, we’ll let Mallozzi take it from here:

When the sister city appears, Atlantis launches its jumpers and drones. Their opponent responds in kind. The most epic battle in Stargate history is joined. Sheppard skillfully pilots his jumper into the heart of the enemy city and lands on a pier. His team disembarks, Asuran weapon in tow, determined to finish the job they set out to complete last episode. But they’re on the clock and running out of time, facing down enemy soldiers and drone strikes as they desperately seek to set up the Asuran weapon as close to critical systems as possible. But they’re not the only ones running out time. Atlantis, outgunned by a foe that has been preparing for war, suffers heavy damage. Even if our team succeeds in their mission, it looks like it will be a pyrrhic victory.

And then — a fleet of hive ships drop out of FTL and concentrate their fire on the enemy ship. It’s Todd. He and his fleet take the pressure off Atlantis, buying Sheppard and his team enough time to initiate the Asuran weapon and retreat back to the Jumper, making good their escape as, behind them, the weapon initiates, setting off a chain reaction of explosions that claim the enemy city. Atlantis returns to the planet’s surface. Sheppard thanks Todd. Wraith and human achieve an “understanding.” And peace finally returns to the Pegasus Galaxy.


Or, maybe the network gods smile upon Stargate Atlantis and renew it for a seventh season, and before the Wraith’s arrival the writers leave us on another impossible cliffhanger!

A special thanks to Joseph Mallozzi for sharing this breakdown of Stargate Atlantis‘s lost season! Be sure to follow him on Twitter and visit his daily blog at