5 Best Stargate Atlantis Episodes, Ranked

Recent weeks have been tough on diehard Stargate fans, who were heartbroken to hear that development of a new series in the franchise, greenlit by Prime Video in 2025, had been canceled. Although many of us still hope for more Stargate in the future, there's a comfort in knowing we can always revisit the old adventures, especially "Stargate Atlantis." That's why we've put together a list of the five best episodes of the show, perfect to binge whenever you need a quick trip through the gate.

The first "Stargate SG-1" spin-off, "Atlantis" carries over from the original series' multi-part backdoor pilot — consisting of Season 7's "Lost City" and Season 8's "New Order" — as Stargate Command sends the Atlantis Expedition into the previously unknown Pegasus Galaxy. Initially led by Dr. Elizabeth Weir (Torri Higginson) with the help of major-turned-colonel John Sheppard (Joe Flanigan), the Expedition discovers that while there are human cultures out there worth connecting with, the vampiric Wraith could wipe out all life in the Milky Way.

While the Stargate franchise timeline is a bit messy, "SGA" offers some of the best episodes the brand has to offer. For many, it's considered the best of the three main Stargate programs (here's the correct way to watch them) due to its riveting premise, superior special effects, and daring cast members. While we (sadly) can't list all our favorites here, these five episodes are perfect for longtime fans and are consistently ranked as some of the most popular with viewers. So dial up the gate, because we're headed back to the Pegasus Galaxy for the greatest hits of "SGA."

A glimpse of Dr. Rodney McKay (David Hewlett) at both his best and his worst, Season 3's "Tao of Rodney" begins with the eponymous character receiving an almost god-like upgrade after he makes explosive contact with an Ancient device. Not only does McKay receive some superhuman abilities in the aftermath, but he discovers that his intelligence has increased exponentially. The only problem is that the Ancient device was meant to help the old race achieve Ascension — meaning that, if McKay doesn't learn to ascend himself, he will die.

"Tao of Rodney" forces McKay to come to the end of himself. While his newfound abilities only increase his ego, the good doctor is forced to be humbled by the spiritual aspects of his predicament that force him to take a few steps back. For perhaps the first time, McKay begins to show genuine interest in the lives and experiences of others, taking the time to share with Weir a book of all her accomplishments, heal Ronon Dex's (Jason Momoa) deep scars, enjoy tea with Teyla Emmagan (Rachel Luttrell), and even compliment Dr. Radek Zelenka (David Nykl).

When it comes to McKay-centric episodes, it's hard to pick one over the other. David Hewlett is an incredible actor who also delivers profound McKay performances in episodes like "McKay and Mrs. Miller" from earlier this same season and Season 5's "The Shrine," both just as beloved by fans. However, it's "Tao of Rodney" that sticks with us as arguably the best of the bunch, due to McKay's unfiltered superhuman ego that is so masterfully knocked down a few pegs.

With a title pulled directly from "Hamlet," an episode like Season 4's "Be All My Sins Remember'd" certainly has to rise above. Technically the second section of a three-part story that began with "This Mortal Coil" and ends with "The Spoils of War," this breakout hour of "SGA" stands out for a few reasons. For one thing, it delights us with the biggest space battle in the entire franchise, rivaling even the best of "Battlestar Galactica." As the Wraith and the Travelers work alongside our heroes against the Asuran Replicators, the episode reminds us how far the Expedition has come.

"Be All My Sins Remember'd" is a complex, riveting hour that emphasizes the ways in which "SGA" has grown in just four short years. With the Expedition now under the command of Colonel Samantha Carter (Amanda Tapping), it's no wonder that the stakes now feel higher. With upgraded weapons systems, the Daedalus and the Apollo prove invaluable to the war against the Replicators, and as "Atlantis" closes this plotline out for good, it does so with a wave of satisfaction, capped by a surprise cameo from the long-lost Elizabeth Weir.

Few episodes are as important to "Stargate Atlantis" as "Be All My Sins Remember'd." For one thing, aside from bringing the Replicator arc to a close, the "enemy of my enemy" alliance between the Expedition and the Wraith known as "Todd" (Christopher Heyerdahl) is one of the more nuanced plotlines in the series. For more "SGA" episodes that boast epic, narrative-driven battles, Season 1's "The Eye" and the series finale, "Enemy at the Gate," are great as well.

When it comes to season finales, "Stargate Atlantis" always knew how to do them right. Season 4's "The Last Man" comes right on the heels of the climactic "The Kindred" two-parter, as Col. John Sheppard enters a stargate exactly as a solar flare occurs, which transports him 48,000 years into the future. Not only has Atlantis been long abandoned, but New Lantea has undergone a series of climate changes so that its once-sprawling seas are now a harsh desert. With the help of an A.I. version of an elderly McKay, Sheppard fights hard to return to his time.

"The Last Man" is pretty much a perfect "SGA" episode. As Sheppard wrestles with his latest predicament, he learns the fate of all his companions, who were largely killed by the hybrid Michael (Connor Trinneer). It's here that we get a small glimpse into the future of "SGA," as certain elements from this timeline would later be folded into the fifth and final season, such as Richard Woosley's (Robert Picardo) takeover from Carter as leader of the Atlantis Expedition. Of course, the reason this episode is so memorable is due to Sheppard himself, whose persistence always sees him through.

The finale ends on a cliffhanger that gets resolved in the fifth season premiere, "Search and Rescue," though "The Last Man" is a great standalone watch as well. Sheppard-centric episodes, such as Season 3's "Common Ground" and Season 2's "Epiphany," are always a hit, as Joe Flanigan's swashbuckling charisma carries the character no matter his latest circumstances. It's a shame "Stargate Atlantis" was eventually canceled, because he's the kind of military sci-fi hero that can't be kept down.

There perhaps isn't a more gut-wrenching episode of "Stargate Atlantis" (maybe even the whole Stargate franchise) as Season 3's "Sunday." What at first appears to be a simple "day in the life" episode, highlighting what the crew of the Expedition do on their day off, quickly takes a hard turn when an explosion rocks the city. Leaving three dead, the team works overtime to dismantle the Ancient weapon at the center of the tragedy — ultimately leading to the death of fan-favorite Dr. Carson Beckett (Paul McGillion), who risks his life to ensure Atlantis' survival.

There are some great moments peppered throughout "Sunday" that offer us some added insight into our heroes. Sheppard and Ronon reveal their tragic relational histories, Weir gets caught up in a potential office romance, it's hinted that Teyla has romantic interest in one of the Athosians, and McKay does everything humanly possible to get out of going fishing with Beckett. Of course, with Beckett's shocking demise, McKay's refusal to spend the afternoon with his best friend is even harder to swallow.

"Sunday" ends with a powerful moment in which McKay plays out a final conversation with Beckett in his mind that brings the audience to tears. Though Beckett would be replaced by Dr. Jennifer Keller (Jewel Staite), and a Beckett clone would appear in the final two seasons, "Sunday" is a harrowing reminder of how dangerous the Atlantis Expedition always was. Although there isn't another episode quite like it, fans may also enjoy revisiting Season 2's "Michael" or Season 5's "The Daedalus Variations" for their like-minded non-linear storytelling.

This is a bit of a cheat, because "The Siege" isn't just one episode of "Stargate Atlantis," it's actually three. The final two episodes of the show's breakout first season and the Season 2 premiere make up this consequential trilogy, as the Wraith declare war on the Atlantis Expedition by attacking their newfound home. The whole thing is a masterful climax to everything that's been set up since the two-part series premiere, "Rising," and it's here that "SGA" changes forever.

Not only is "The Siege" arguably the last time the Wraith felt truly menacing as a united collective, but the stakes are high on all fronts as Sheppard and Weir struggle to wrest control of Atlantis from Marine Colonel Dillon Everett (Clayton Landey). With a brilliant combination of sci-fi action and emotional suspense, "The Siege" (especially "Part 2") is a thrilling head-first dive into intergalactic warfare that pushes everyone on the Expedition to their limits, including Lt. Aiden Ford (Rainbow Sun Francks), who changes on a genetic level following his close encounter with a Wraith warrior.

The first three-part "Stargate Atlantis" adventure, "The Siege" certainly lives up to its name. Although the show was still finding its sea legs in that inaugural year (Ronon had yet to join the "Stargate Atlantis" cast), it was here that the program became just as grand as "SG-1." For more great "SGA" episodes, don't sleep on Season 1's "Letters from Pegasus," Season 4's "Midway," and "Tabula Rasa."