It has been 13 years since Stargate Atlantis left our TV screens, and the show’s abrupt ending still stings for long-time fans of the series.

What ended up being the final season was one of Atlantis‘ best, with new creative energy and new directions in the story: villains from a parallel universe, antagonistic Asgard, Replicators who claimed to be good guys, Todd the Wraith growing in power and influence, a coalition of planets in the Pegasus Galaxy seeking to hold our team accountable for their actions … and so much more.

In Season Five there was a new expedition leader (Richard Woolsey, portrayed by fan-favorite Robert Picardo). And the writers were delivering stellar hours of sci-fi television — from “The Shrine” and “The Daedalus Variations” to Daniel Jackson’s appearance in the mid-season two-parter, to the alternate reality “Vegas”, and the explosive finale, “Enemy at the Gate.”

That last hour of Atlantis was actually the show’s 100th episode. It brought the Ancient city all the way to Earth, in order to defend the planet from a Wraith super-hive (thanks to a previously unknown piece of technology, the wormhole drive). When the curtain fell the city was parked outside of San Francisco Bay, Todd was a prisoner, and Earth was safe … for now.

But “Enemy at the Gate” wasn’t written to be a series finale. The show wasn’t meant to end here. And in a conversation with “Dial the Gate,” Stargate Atlantis writer and executive producer Joseph Mallozzi talked about what was in the works — and what he hoped a sixth season would have achieved.

“Atlantis is going to make its way back to Pegasus, and en route they end up experiencing engine problems,” Mallozzi said. “And they end up stranded between Pegasus and the Milky Way in another galaxy. And they end up detecting a power source coming from a world … and ultimately the story that unfolds ended up laying seeds for what would [instead] be the Stargate Universe story [‘Common Descent’ and ‘Epilogue’],” where our team meets their own descendants.

Listen to the full breakdown in this clip from Mallozzi’s conversation with host David Read:

Network renewal is always an uncertain business, and while Season Five was in production series co-creator Robert C. Cooper made a forward-thinking suggestion. According to Mallozzi, Cooper recommended pitching MGM on expanding the episode order from 20 to 22. That would allow them to cap off the 2008 production calendar with a 2-parter, and if the show was cancelled the first Atlantis movie would already be in the can. If the series was renewed by SCI FI, “Extinction” would become a 2-parter to kick off Season Six.

“That’s something we pursued that never gained traction, unfortunately,” Mallozzi said. “But in hindsight I wish we really pushed a lot harder.”

After the show was cancelled the story became Stargate: Extinction. MGM commissioned Mallozzi and Paul Mullie to write a film script, and SCI FI announced it would air the movie after its premiere on DVD.

Extinction would have seen Atlantis on a wild, time-travel trip back to the Pegasus Galaxy. Along the way the team would be waylaid in another galaxy, and also encounter a more hostile version of Todd from the future.

“It was a lot of fun,” Mallozzi said. “… It was such a great Todd episode, as well. Basically you have the present-day Todd, who is locked up, who encounters a future version of himself — who has designs on the planet, and designs on Atlantis.”

The script for the film went on the shelf in 2009 (due to softer than hoped for DVD sales from SG-1’s two films, The Ark of Truth and Continuum), and in 2010 MGM declared bankruptcy. Spin-off Stargate Universe was cancelled, and it became clear that Extinction wouldn’t be made.

“Between the time those [SG-1] direct-to-DVD movies were released and we sent in our script for Stargate: Extinction, the DVD market had died,” Mallozzi said. “Essentially the bottom had fallen out. And MGM decided to shelve the production on the movie.”

Be sure to watch the clip above to hear more about what was planned for Stargate Atlantis Season Six, including a big role for Teyla and a story that would have brought back another popular villain in a big way. “Dial the Gate” also recently hosted Mallozzi and Mullie together for a brand new interview about their 11 years working on the franchise.