- This episode is part 1 of 2; it is followed by "Search and Rescue".
While searching for Teyla Emmagan, Lt. Colonel John Sheppard gates to Atlantis, only to discover it's been completely abandoned with John being left stunned when a hologram of Dr. Rodney McKay informs Sheppard that he's traveled 48,000 years into the future, a future where the Wraith Michael reigns supreme.
On M4S-587, Lt. Colonel John Sheppard and Major Evan Lorne wait for their Genii contact, where he claims to have information regarding Teyla Emmagan, who was kidnapped by Michael Kenmore. However, the contact doesn't turn up, and they try to decide whether the Genii are reliable. On the one hand, they tried to have Harmony killed, but on the other, Ladon Radim didn't order the hit, and is trying to get on their good side. With time running out, Sheppard gates back to Atlantis, leaving Lorne to stay for a while in case the contact does show up. Sheppard returns to Atlantis. However, the city is different; it is empty, with no power on at all, as well as a glow of red from the daylight and a higher temperature. He calls out, but nobody answers. He decides to look outside, but has trouble opening the door. When he does, he sees that the oceans have mysteriously turned to desert.
Sheppard desperately tries to activate the city's systems, but can't. He then hears static, and hears a voice, Dr. Rodney McKay, who wants to know of Sheppard's position, and what has happened. He then tells him to go to the Holo room.
Sheppard runs there, and activates the projector, where an aged McKay materializes. He tells Sheppard that he is a hologram of himself from 25 years since Sheppard was missing. He also relates that Sheppard was involved in a freak accident involving a solar flare, similar to the one where SG-1 was transported to the year 1969, but instead of traveling back in time, he went forward in time, by 48,000 years, likely making Sheppard the last man alive in the Pegasus Galaxy and quite possibly in the entire universe.
Fortunately, the hologram of McKay didn't just come to chat with Sheppard. Instead, he has a plan to send Sheppard back to 2008, by waiting for a similar solar flare to send him back. The problem is that he would have to be placed in a stasis pod for at least another 800 years. This is the only chance, since if he returns later than two months since he was missing, it would be too late. McKay reveals that two months after Sheppard disappeared, they announced him KIA and had a funeral, without Sheppard's body. The team later received solid intelligence on one of Michael's labs, where they finally found Teyla Emmagan, who had delivered her baby, but later that Teyla was dead, Michael having killed her.
Michael then used the baby to perfect his Hybrids, and later administered the Hoffan drug on every single planet in Pegasus. The Atlantis expedition, with their limited personnel attempted to lessen the mortality rate of the drug, but were unsuccessful. With the Wraith's food supply tainted, their civil war went into full swing, and within a year, the Wraith were brought to their knees. Michael's army captured a Wraith Queen, where he told her that when he escaped from the Humans, he expected a warm welcome back, but was met with scorn instead. With his anger, he personally decapitated her and showed her head to his army.
Now that Sheppard is aware of the situation, he realizes that if he rescues Teyla, he can stop all this from happening. However, on their way to the stasis room, he and McKay see the corridor is blocked off by a mountain of sand, and there is no other way out. The only other option is a trek across the sand to a nearby tower but Sheppard can't walk across the sand due to a sandstorm that is raging outside. He decides to wait it out, while Holo-McKay tells him what happened to the others. He explains that with Michael in control of the galaxy, the International Oversight Advisory were hesitant in giving out resources to help stop him. However, Colonel Samantha Carter didn't take no for an answer. They handed her a new Daedalus class ship, the Phoenix. Since it was barely off the assembly line, Carter, McKay and Dr. Radek Zelenka worked tirelessly and finished installing the Asgard systems on the ship. After they were finished, Carter told McKay to return to Atlantis, while she would strike back at Michael.
Carter and the crew performed several guerrilla-style ambushes, where they would exit hyperspace, strike at Michael's Hive Ships, and jump out again. Despite terrible odds, Carter inflicted considerable damage to Michael's fleet. However their luck soon ran out. They found intelligence that Michael will strike at a planet, not knowing Michael's army supplied Carter with misinformation. When the Phoenix arrived, the ship was ambushed, and several systems, including the Asgard plasma beam weapons went offline. The Phoenix fired conventional nuclear warheads, but did not cause much damage. With the ship's hyperdrive and other engines reaching critical, Carter evacuated the entire crew. With the transporters down, Carter was left with little choice but to set a collision course for one of Michael's Hives. The Phoenix charged into a Hive Ship, where the force of the explosion destroyed the other two attacking Hives but also costing Carter her life.
Back in the future Atlantis, Holo-McKay has discovered why the ocean turned to desert; the Star is dying, turning into a red giant which heated the planet so much that in 500 years time the atmosphere will burn, which will kill Sheppard the second he exits stasis. Sheppard decides to use the city's solar panels to power the shield (although most likely it was collapsed to protect only a small area) along with the Naquadah generator, which will buy them enough time for Sheppard to return to the present. Then, since he can't wait due to hunger, he covers his face and attempts his walk across the harsh desert. He pressures McKay to keep talking, by asking what happened to Ronon Dex.
After the death of Teyla and the apparent death of Sheppard, Ronon no longer felt welcome in Atlantis, and left. He learned that Michael was planning to convert the populations of the stronger worlds into Hybrids, and destroy the weaker civilizations. Ronon planned and developed an army to take down Michael. With the galaxy in a state of panic, he didn't have trouble finding volunteers. The recruits were mainly farmers, but Ronon taught them every assault tactic he could. The Atlantis expedition also supplied them with Earth weapons, particularly C-4 and FN P90 Personal Defense Weapons. After he felt his newly-created army was ready to fight, they embarked on several operations against the Hybrids.
In one particular mission, they attempted to destroy one of Michael's labs. There, they ran into an old friend, "Todd" the Wraith, who also planned to destroy the base. When they heard that Michael's reinforcements were zeroing in on the base, Ronon evacuated his army while he and "Todd" planted C-4 to destroy the base, but wishing to allow his forces to escape, the two held off the Hybrids until Ronon's soldiers radioed him that they had evacuated. With no way out, Ronon and "Todd" decided to detonate the C-4, where they shared a smile with each other before Ronon detonated the explosives, killing them all and destroying the base.
Sheppard, having survived the trek, is unconscious. After a whole night, he wakes up, and quickly agrees they should go to the stasis pod. They arrive in the stasis room, where Holo-McKay tells him to take a crystal, containing the address to the planet where Michael plans to kill Teyla. Before he steps in, Sheppard wants to know what happened to McKay. Dr. Jennifer Keller planned on a mission to help more lives in the galaxy, only to be stopped by the new Atlantis leader, Richard Woolsey. He told her that since Michael's forces had taken over the galaxy, the IOA ordered all resources to be pulled for the protection of the city. Disgusted by this, Keller quits the expedition. McKay decides to quit as well, and both leave on the Daedalus back to Earth.
During their time, the two grew closer and closer, until by the time they returned to Earth, they weren't just colleagues any more, and were seeing each other. Over the next year, McKay got a high paying job in an aerospace engineering firm, while Keller headed her own medical practice. Things were fine between them until Keller fell ill. When she turned to Stargate Command, the doctors discovered traces of the Hoffan drug in her systems, and told her that she was dying. With this, McKay had a revelation to prevent the whole thing from happening. However, Keller told him to stop, since there is no point in chasing after something that is already gone. She died three days later.
He got a job teaching physics at the local college which gave him the time he needed to develop a way to predict solar flares. He got help from his sister, Jeannie Miller, but after a while she gave up helping and told Rodney to stop as well. After 25 years he found a way and presented the idea to Major General Evan Lorne, who was then in charge of the SGC. He convinced Lorne to take him to Atlantis to enact his plan. After McKay finishes explaining this, Sheppard enters stasis.
Back in the present, Atlantis' Stargate activates, where Chuck reads Sheppard's IDC. Sheppard returns, and discovers that he has returned after 12 days since he went missing. He tries to convince Carter of the news that he can find Teyla, but she finds this far-fetched. When McKay notices the solar flare, they believe Sheppard is telling the truth. Carter sanctions the mission to M2S-445, the planet Michael is planning to kill Teyla. Lorne joins Sheppard's team.
On M2S-445, the teams arrive in Michael's base, where they split up. Sheppard and Ronon find a room, with several brutal surgical implements. Sheppard observes that this is the "sick, twisted version of a maternity ward", which means this is the room where Michael plans to both deliver the baby and kill Teyla. Meanwhile, McKay and Lorne enter another room, where McKay finds a relic computer. There, McKay discovers that the information is Michael's database, containing his Hybrid research and planets where he is conducting the research. For a moment, the team is excited at the prospect of Michael's downfall, until the computer shuts down, and a timer activates. The base is booby trapped, and while the teams desperately try to run, they are too late. The base collapses in on them, leaving the teams trapped.
Holo McKay: (over radio) Look, I need you to describe exactly what you're seeing. Where are you?
Sheppard: I'm in the Control Room, it's deserted.
Holo McKay: Is there any power?
Sheppard: No, everything's dead, and, oh yeah, did I tell you the ocean's gone?
Holo McKay: Sorry, what?
Sheppard: The big blue thing out the window. It's gone. It's, it's, it's a desert, and it's about a hundred and twenty degrees in here.
Holo McKay: Oh, jeez, the planet must have undergone some serious climate changes.
Sheppard: You're telling me I just traveled forty eight thousand years into the future in ten seconds?!
Holo McKay: I know, it is kind of cool when you think about it, isn't it?
Sheppard: Surfing a thirty-foot wave in Waimea is cool! Dating a supermodel is cool! This is not cool!!
Holo McKay: There's not enough power for you to gate back to Earth, and without a MALP, going anywhere else would be far too risky. It is entirely possible that you are the last human being alive.
Sheppard: You're not doing a very good job of cheering me up here.
Holo McKay: Oh, consider yourself lucky, young man.
Michael: You know the irony is that I never asked for any of this.
(Encountering their way is blocked)
Holo McKay: The sand has penetrated the lower levels.
Sheppard: 48,000 years into the future, you've still got a knack for stating the obvious. All right, what do we do?
Holo McKay: I don't know.
Sheppard: What do you mean, you don't know?
Holo McKay: Well, I wasn't programmed for this variable!
Sheppard: You said you had twenty five years to work on this plan!
Holo McKay: Well, McKay did, and he brilliantly anticipated a lot of potential problems! It's just that, well, this wasn't one of them.
Woolsey: Michael knows the defensive capabilities of this base and our ships. The I.O.A. thinks it's highly unlikely he will launch an unprovoked attack.
Keller: So, that's it, then? We're supposed to just stand back and let him take over the rest of the galaxy?
Woolsey: How many more of our own people have to die, Doctor? Colonel Sheppard, Colonel Carter, Ronon, Teyla – they were your friends.
McKay: Sheppard is not dead.
Woolsey: Right. He's just been transported forty eight thousand years into the future. I guess that makes him one of the lucky ones.
(Sheppard runs through the gate, holds up his hands to the Marines)
Sheppard: Colonel. It worked. It worked. Rodney, you're a genius.
Carter: John, what happened?
Sheppard: How much time has gone by?
Carter: You've been missing for twelve days.
Sheppard: (to himself) Twelve days, twelve days, okay, she wouldn't have had her baby yet. (to Carter and McKay) Look, I know this sounds kinda weird but we're on the clock.
Carter: John, what are you talking about?
Sheppard: I know where Teyla is.
McKay: Look, I know you have been debriefed about all the future events, all the things we have to avoid, but there is one more thing I need to know: Do I still have hair?
- Joe Flanigan as Lt. Colonel John Sheppard
- Amanda Tapping as Colonel Samantha Carter/Samantha Carter
- Jason Momoa as Ronon Dex/Ronon Dex
- David Hewlett as Dr. Rodney McKay/Rodney McKay
- Jewel Staite as Dr. Jennifer Keller
- Christopher Heyerdahl as "Todd"
- Connor Trinneer as Michael Kenmore
- Kavan Smith as Major Evan Lorne/Major General Evan Lorne
- Kate Hewlett as Jeannie Miller
- David Nykl as Dr. Radek Zelenka
- Robert Picardo as Richard P. Woolsey
- Andee Frizzell as Wraith Queen
- Chuck Campbell as Chuck
- Heather Doerksen as Major Pat Meyers
- Kory Grim as Recruit
- Christian Sloan as Human-Wraith Hybrid
- Dan Kashagama as Doctor
- Gerry Durand as Captain Frank Levine (Uncredited)
- Uros Certic as Marine (Uncredited)
- D. Harlan Cutshall as Marine (Uncredited)
- Mario Ferrante as Marine (Uncredited)
- Bill Y.W. Butt as Doctor (Uncredited)
- Lalo Espejo as Scientist/Scientist (Uncredited)
- Lani Gelera as Female Combat Volunteer (Uncredited)
- Rob Boyce as Combat Instructor (Uncredited)
- ? as Teyla Emmagan
- ? as Jennifer Keller's father
- ? as Marine
- This is the first and only episode in which a Wraith Hive ship is destroyed by Asgard plasma beam weapons, even though it happened in an alternate timeline.
- This episode contains the most Hive ships seen destroyed in a single episode, namely six, even if it is just a semi clip-show of an alternate timeline.
- Dr. Rodney McKay mentions Mark XII series Naquadah generator, which was so advanced that only one of them was needed to power the shield of Atlantis (which normally requires at least one Zero Point Module to function) for almost 800 years.
- New Lantea's sun must be quite old if it turns into a Red giant in 48,000 years. Sol will take several billion years to do the same. Given that main-sequence stars like New Lantea's or Sol take, as far as scientists know in the real world, several billion years to go through their yellow dwarf phase (i.e., where the Sun, and apparently New Lantea, is now), it is quite serendipitous that New Lantea turns into a red giant in less than 50,000 years - perhaps one hundred-thousandth or less of the normal span of the yellow dwarf phase.
- Other instances in which a solar flare sends a traveler backwards or forwards in time are the Stargate SG-1 episodes "1969" and "2010", the Stargate Universe episodes "Time" and "Twin Destinies" and Stargate: Continuum. In previous episodes regarding solar flares and time travel, the traveler was sent back to the planet they left from. In this episode, Lt. Colonel John Sheppard emerges at his destination. That is because in those instances the solar flare originated from the outbound gates sun, in this instance the solar flare came from the inbound gates (New Lantea's) sun.
- This episode contains the first appearance of the Phoenix, albeit in another timeline.
- In Major General Evan Lorne's office, the portrait of Atlantis that he was painting in the episode "Sunday" can be seen hanging on the wall. This is the second time that Lorne has been seen in an important position in an alternate reality or alternate timeline. The first was in the Stargate SG-1 Season 10 episode "The Road Not Taken" in which he was leader of SG-1.
- The episode shares its title with a science-fiction novel called The Last Man by Mary Shelley which is a story about the last human alive on Earth.
- Sheppard was originally supposed to return to an ice-covered Atlantis instead of the city covered in sand. But since the Stargate SG-1 movie Stargate: Continuum was partly shot in the Arctic the imagery would have been too similar. Therefore, the Ice Age was changed to a period of extreme heat due to the sun turning into a Red giant.
- According to Paul Mullie, this episode was originally supposed to end with Sheppard saying "I know where Teyla is", but Syfy insisted there be another scene afterwards where the team attempt a rescue and get trapped, leaving more of a cliff-hanger.
- During filming of this episode, David Hewlett and his wife Jane had their newborn son, Sebastian "Baz" Flynn Loughman Hewlett.
- No mention is made of Dr. Carson Beckett's fate in the alternate timeline. Presumably, McKay's hologram knew what ultimately happened to him, but his fate is never revealed to Sheppard.
- This is the third season finale in the Stargate franchise to feature Time Travel. The first being "Moebius, Part 2" and the second being "Unending".
- At the beginning, Sheppard and Lorne refer to the events of the episode "Harmony".
- SPOILER: Several of the events from the alternate timeline seen in this episode ultimately come to pass: Richard Woolsey becomes the leader of Atlantis, McKay and Dr. Jennifer Keller begin a romantic relationship and Colonel Samantha Carter becomes the commander of the George Hammond, the current timeline version of the Phoenix which is renamed after Lt. General George S. Hammond dies of a heart attack.
- In Stargate Atlantis: Allegiance, Carter faces a similar fate to her alternate timeline self from this episode: seeing no other choice during the Battle over the Outer Rim Planet, Carter beams her crew out of the George Hammond and attempts a suicide run. However, this time she is interrupted when the Daedalus is able to reenter the battle and help her destroy the enemy Hive ship. She nearly dies anyway due to lacking her transport system as in this episode, but is beamed out by the Daedalus instead at the last moment.
- SPOILER: At this point in the series, the producers had no plans to make Richard Woolsey the base commander for season five as they believed Amanda Tapping would return. It turned out to be remarkable foreshadowing as Robert Picardo did end up joining the main cast due to Tapping leaving to executive produce and star in Sanctuary.
- This is the last of seventy-eight episodes of Stargate SG-1 and Stargate: Atlantis directed by Martin Wood.
- Rachel Luttrell did not appear in this episode. A body double was used for the one scene she was in and Martin Wood used creative camera angles to show as much of the body double as possible without making it clear that it wasn't Luttrell.
- Andee Frizzell (Wraith Queen) previously played the Wraith Keeper in the Stargate: Atlantis episode "Rising", Wraith Queen (The Hive) in the episodes "The Lost Boys" and "The Hive", Wraith Queen (Michael's hive) in the episodes "Allies" and "No Man's Land", Wraith Queen (Submersion) in the episode "Submersion" and Wraith Queen (Spoils of War) in the episode "Spoils of War".
- The Stargate at the start of the episode appears to contain glyphs on both sides (the side facing the screen being the back). In fact, the back appears to be a mirror copy of the front. As it has been established that Stargates have a unique backside, which lack glyphs, this is likely an error resulting from the gate being CGI.
- After dialing the Stargate at the beginning, Lt. Colonel John Sheppard fails to send his Iris Deactivation Code despite the fact that he's going to Atlantis, and even if he had sent it off-screen, his GDO wouldn't have received a confirmation that the shield had been lowered from Atlantis, as he had connected to an abandoned Atlantis.
- When Dr. Rodney McKay's hologram has a discussion with Sheppard in the Holo room his face appears to have aged decades while his hands remain those of a much younger man.
- On her deathbed, Dr. Jennifer Keller mentions "the year I spent in Atlantis." However, Keller spent around two years there because McKay mentioned that "within a year" Michael had brought the Wraith to their knees and Keller only left after the change in leadership.
- When Michael Kenmore presents the head of the Wraith Queen to his Hybrid army, (13:01) it's noticeable that many of people in the crowd are digital duplicates.
- Hungarian: Az utolsó ember (The Last Man)
- German: Der letzte Mann (The last Man)
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