(15) McKAY AND MRS. MILLER

The show’s third season introduced Rodney McKay’s sister, Jeannie. Written by Martin Gero, “McKay and Mrs. Miller” is a heartwarming story about family, forgiveness … and a transdimensional portal. Jeannie helps Rodney and Radek create a bridge to another reality, only to have another version of McKay — “Rod” — come through from the other side. Oh, and Amanda Tapping (“Samantha Carter”) puts in a guest appearance to boot!

This is also the episode where we learned Rodney’s real first name: Meredith.

Did You Know? The episode was made all the more special by the casting of Kate Hewlett, actor David Hewlett’s real-life sister. (Her husband Kaleb is also played by Gero’s long-time collaborator Brendan Gall.)

(14) THE SIEGE, PART 2

The climax of Season One (and, amazingly, the only episode from the first two seasons to make this list) is all-out war, as the Wraith arrive over the skies of Atlantis and lay siege to the ancient city. The great dome shield is up, but it won’t last forever — and the team’s fire power for fighting back is limited.

The season finale comes at the end of a multi-episode arc, and leaves our heroes in mortal danger in its multiple cliffhangers. The visual effects here are spectacular, as night falls and the city’s newly installed rail guns try desperately to repel the onslaught of Darts. The Wraith have beamed foot soldiers inside the city, Lt. Ford is in a stand-off with the enemy, and John Sheppard is piloting a Genii nuke toward the enemy hive ship on a suicide mission.

Did You Know? Writer Joseph Mallozzi reveals that the role of Colonel Dillon Everett was written for Ben Browder (who had not yet been cast as Cameron Mitchell). But at the time Ben was busy shooting the Farscape miniseries. Everett’s fate would have been different had Ben played the role.

(13) LIFELINE

Atlantis‘s fourth season kicked off with a heart-pounding two-parter. After keeping the city alive in deep space in “Adrift,” Sheppard and his team take a Jumper on a desperate mission to steal a Z.P.M. power source from the Replicator home world of Asuras. Dr. Weir is along for this mission, as her life was recently saved by Replicator nanites — allowing her to connect wirelessly to the network that controls the Replicator collective.

“Lifeline” is bitter-sweet, though: Elizabeth Weir sacrifices herself, using her ability to keep Oberoth (guest star David Ogden Stiers) and the Asurans frozen while the others make their escape. This episode also starts the arc that will run through the first half of the season, when McKay activates the Replicators’ core programming that causes them to attack the Wraith.

(12) THE PRODIGAL

The culmination of Michael’s Wraith-human hybrid storyline came late in the show’s final season. Michael (guest star Connor Trinneer) is convinced that Teyla’s newborn child holds the key to his hybrid experiments, and so he boldly invades Atlantis directly. With a group of his hybrids along for muscle, Michael hijacks a Puddle Jumper and uses it to penetrate the city.

Once he is there he hunts Teyla and her baby, but finally loses, falling from the top of the city spire — presumably (but not definitively) to his death.

(10) (tie) THE KINDRED, PART 1

Michael’s obsession with Teyla as the solution to all his problems also took center stage in Season Four. A year before invading Atlantis he kidnapped a pregnant Teyla, studying her and her unborn child to learn how their DNA could help him perfect his hybrids.

Sheppard’s team pulls out all the stops to track and find one of their own … though in Part 2 they ultimately come up short. Teyla remains Michael’s prisoner. Along the way, however, they make a completely unexpected discovery: Michael was also holding captive a clone he made of Carson Beckett (Paul McGillion). Finding their dead friend alive and well again is this episode’s stunning cliffhanger — one of the best surprise punches the show ever delivered.

Did You Know? “What took you so long?” If you hate spoilers on the Internet … well, watch out for SCI FI Channel. The network’s promotional teaser for this episode broadcast that twist ending (including the very last line of dialog, from Carson) a week in advance.

(10) (tie) SPOILS OF WAR

The destruction of the planet Asuras in the climactic battle of the war with the Replicators left more than devastation and debris in its wake — it also left treasure. The Asurans left behind technology, especially the super-rare and useful Zero Point Modules. In the following episode the team discovers that, in the midst of the battle, Todd the Wraith (guest star Christopher Heyerdahl) has stolen the tech out from under their noses.

When the Atlantis team pursues the Wraith they find a secret experiment — a laboratory where Todd is cloning hundreds of thousands of Wraith in preparation for a new civil war. We learned a lot about the Wraith in this episode, including their ability to interface their tech with Ancient technology. We also see a Wraith birth, and for the first time witness a Wraith feeding on the life force of another Wraith.

(9) TAO OF RODNEY

This stand-out McKay episode sees Rodney gain enhanced abilities (superpowers, that is) after being exposed to a long-buried Ancient experiment. He can read minds, heal with a touch, and even levitate donuts! But of course there is a catch: Rodney’s human body can’t handle the upgrade, so now he is going to die … unless he can find a way to “release his burden” and ascend.

Did You Know? The “ascend-o-meter” monitoring system that Rodney uses in the episode may have been developed originally by Anubis, who was attempting to create an advanced human host body. SG-1 first discovered the device in the episode “Prototype.”

(7) (tie) THE LAST MAN

Season Four’s final episode was high-concept sci-fi, and at the same time a more intimate story. A solar flare sends John Sheppard some 48,000 years into the future, when Atlantis is abandoned and the ocean has been replaced with scorching sand dunes. He has only a hologram of an older Rodney to keep him company — and to hatch a plan to send Sheppard back to his own time. Along the way Holo-Rodney tells him about his timeline … including the heart-breaking deaths of their friends.

Along with those flashbacks “The Last Man” has a bit of everything: space battles, time travel, an unstoppable foe, romance (Rodney hooked up with Jennifer Keller), and a chance to undo a dark future. And it’s a season finale — so, of course, there is a cliffhanger.

Did You Know? Although flashbacks show Richard Woolsey (Robert Picardo) in command of the Atlantis expedition, he hadn’t been cast for the role that would become permanent in Season Five. When this episode was written, producers assumed that Amanda Tapping would return the following year as Samantha Carter.

(7) (tie) THE RETURN, PART 2

Also coming in with the same fan score is Season Three’s mid-season premiere — another big one in the Replicator storyline. After discovering the existence of Atlantis the Asurans send a strike force to take the city. By now the expedition members have returned home to Earth, with the city taken over by surviving Lanteans. They are no match for the Replicators, who take control of the city and put Richard Woolsey and Jack O’Neill (guest star Richard Dean Anderson) into confinement.

In Part 2 Sheppard’s team steals a Jumper from Stargate Command and returns to the Pegasus Galaxy, reuniting with Teyla and Ronon to take back their home. This requires going toe-to-toe with the Replicators, suffering a few hands in the forehead, and a deep dive for RDA in a memorable underwater sequence.

(6) FIRST STRIKE

After they fail to hold the city, the Replicators begin to build a fleet of ships — which Earth reconnaissance detects in the third season finale. The command decision that comes down from the top goes against our team’s instincts, but it happens anyways: a preemptive first strike, with the Apollo attacking Asuras with a massively destructive weapon.

In response the Asurans send a satellite weapon to attack Atlantis, with a constant beam that forces the city to dive deep under the ocean … and ultimately to fire up the city’s stardrive and flee the planet altogether.

Did You Know? This is Jewel Staite’s first appearance as Dr. Keller, a role that would become permanent in Season Four. But she previously appeared on the show under prosthetics, as the Wraith girl Ellia (“Instinct”).

(5) THE RETURN, PART 1

Time for the Top 5!

Season Three’s mid-season two-parter opens in an astonishing way: Daedalus discovers a ship full of living Ancients, who they help return home to Atlantis after 10,000 years. Led by Captain Helia (guest star Megan Leitch), the Lanteans take over the city and ask the Earth expedition to leave. With Woolsey and Jack O’Neill there as ambassadors, the team returns home.

This is a bit of a slower episode, as Elizabeth Weir and her people cope with life back home and the sudden end of their mission. In the end, though, when they learn that Atlantis has fallen to the Replicators, Elizabeth and the team take matters into their own hands and fight to return to the Pegasus Galaxy. That includes a bit of subterfuge (Bill, do you really think Dr. Weir plays World of Warcraft?) and theft, as the first half of the season closes with the team taking a stolen Puddle Jumper into the Stargate.

“Weir was fighting against giving up control of Atlantis, and that was a curious balance to play,” actress Torri Higginson told Steve Eramo. “There’s a sense of propriety of this city that we’ve basically saved and wanting to be part of the Ancients taking it back over, but then being told we couldn’t. At one point I think Weir became a bit too emotionally attached to Atlantis and had to reel herself back in.”

Did You Know? Before she played Helia, Megan Leitch appeared in a prominent role in an episode of Stargate SG-1. She played Ke’ra (who turned out to be a young Linea) in the third-season episode “Past and Present.”

(4) THE LOST TRIBE

The second half of Season Five’s big two-parter brought a massive revelation to the show, one that sent shock waves from the Pegasus Galaxy to the Milky Way: the Asgard are not extinct. A lost tribe, a hidden colony of Asgard who broke away from their people thousands of years ago, is alive and well in Pegasus. They have a ton of advanced technology, and every intention of using it to save the last of their species by any means necessary — even if it means making hyperspace travel impossible.

With Rodney McKay and Daniel Jackson held prisoner by the Asgard, another group from Atlantis must retake the Daedalus from Todd the Wraith (who has hijacked the ship to target the Asgard). And still another group, led by Colonel Sheppard, seek help from the Travelers.

In the end they rescue their friends and put an end to the machinations of the Attero device … but the evil Asgard are still out there, ready to come out of the shadows and make their presence felt.

Did You Know? Though it wasn’t established in canon before the show’s cancellation, writers planned to call this tribe of Asgard the “Vanir” — named for a faction of gods in Norse mythology.

(3) MIDWAY

Always cited as a fan favorite, “Midway” was a Stargate crossover of epic proportions. Getting Teal’c (guest star Christopher Judge) and Ronon Dex (Jason Momoa) together for a one-on-one throwdown was just the beginning. Here we have a close-up look at the shiny, new Midway Space Station, an enemy hacking attack of the gate network, and the Wraith invasion of Stargate Command.

It’s the only time that Wraith foot soldiers ever set ground on Earth soil! But Ronon and Teal’c are also en route (for Ronon’s evaluation by the I.O.A.), and the two warriors end up the last line of defense. They manage to stop the Wraith, of course … but even these two mighty warriors are no match for the idiocy of Peter Kavanagh (guest star Ben Cotton), whose thoughtlessness triggers Midway’s self-destruct. The station goes up in a huge ball of fire.

(2) BE ALL MY SINS REMEMBER’D

The climax of the conflict with the Pegasus Replicators, which spanned nearly a season and a half, came in this phenomenal hour that started the back half of Season Four. “Be All My Sins Remember’d” is commonly cited for its visual effects — an epic space battle that saw human, Wraith, and Traveler ships united in a coalition against the Replicators, in an all-or-nothing firefight over the planet Asuras.

But ultimately it was some brilliant engineering from McKay, Zelenka, and the rest of the team that turned the Replicators’ nanite programming against them.

This episode isn’t great simply because it wraps up this major arc in spectacular fashion. It’s also an episode with some surprising heart. Using the technology that the Ancients originally used to create the Replicators in the first place, Rodney and Radek create their own “Friendly Replicator ANdroid” — “Fran” (guest star Michelle Morgan). But she is an innocent, new life … one they must ask to sacrifice herself in order to save the galaxy.

And, she does. It’s a beautiful piece of writing and acting, which captures the best of what Stargate Atlantis had to offer: adventure, action, effects, lovable characters, and those probing moral dilemmas that make for great science fiction storytelling.

Did You Know? Michelle Morgan was originally cast as Linara, the daughter of the Seer, Season Four’s “The Seer.” She had to back out because of scheduling conflicts with a movie she was shooting, but was quickly recast as Fran a few episodes later.

(1) FIRST CONTACT

Topping the list of all 100 episodes of Stargate Atlantis in GateWorld’s fan poll is “First Contact.” Part 1 of the fifth season two-parter brought Daniel Jackson (Michael Shanks) to Atlantis and introduced an advanced new foe … though we wouldn’t learn until the next episode that the mysterious, armored warriors were, in fact, Asgard.

After Daniel and Rodney discover a secret lab hidden in the city, they begin to catalog a trove of technology and experiments left behind by the Ancient scientist Janus. They inadvertently activate the Attero device, which the Asgard detect and come to retrieve — along with Rodney and Daniel as their prisoners. Armed with fast-moving strike ships that can penetrate the city’s shield, and weaponized suits with personal shield emitters, this never-before-seen enemy seems to be unstoppable.

To make matters worse, Woolsey and Keller’s efforts to advance the alliance with Todd goes south on board the Daedalus. And an explosion inside the city spire leaves fans wondering who will live, and who will die.

“It was the most cryptic, enigmatic pitch of a story I’ve ever heard,” Shanks told The National Ledger. “The pitch was: ‘You go to Atlantis and something happens, and Daniel has to help everybody to get rid of the bad guys that are coming.’ I was like, ‘Wow, did you spend a lot of time thinking that one up?’ But it’s one of those things.

“Stargate is like old home. It’s always nice to be able to revisit that universe and those individuals, and to play that character again.”