In Dr. Daniel Jackson's lab, Colonel Jack O'Neill is trying to solve the crossword puzzle while he still can. Jackson notices O'Neill is not paying attention to anything he tries to have him read, and snatches the puzzle from him. When Major Samantha Carter walks in, Jackson notices that O'Neill has written "Taonas" on one of the solutions, and on another, he wrote "Proclarush". He also notices that the clue for where O'Neill wrote Taonas is "sphere," while the clue for Proclarush is "label". He believes that sphere means planet, and label means the name of that planet.

In the Mess hall, Jackson reads through a book and discovers that "Proclarush Taonas" translates to "lost in fire". However, there is still no Gate address to Proclarush. O'Neill then provides him with a clue; he rips off Jackson's patch containing the Point of Origin symbol, which O'Neill describes as "At". Jackson begins to understand what O'Neill is trying to say and demonstrates by showing him Canis Minor; O'Neill responds with a "shh", and explains that the sound "shh" is what the symbol reminds him of. Jackson's theory may be confirmed; they don't have to look through the list of addresses to find the planet, the names themselves serve as the addresses. Proc-la-ru-sh Tao-nas At would be the full gate address.

Jackson explains it to Dr. Elizabeth Weir in the Stargate Operations room. However, Carter encounters a problem: they already dialed the planet two years ago, but couldn't establish a lock, possibly because the planet's Stargate was buried. Jackson considers using the Prometheus, but with Anubis on his way to Earth, the ship must stay to defend the planet. Instead, the team plans to Gate to Chulak to see if Teal'c and Bra'tac have recruited any ships yet. Meanwhile, O'Neill is in a store room, packing various equipment including Hazmat suits and a Naquadah generator. He cannot explain why he is packing, though the rest of the team thinks that they're on the right track.

On Chulak, Teal'c and Bra'tac are in a tent calling in various Jaffa. One walks in, and introduces himself as Ronan, whose father is known to Bra'tac. He has a Tel'tak at his disposal, but warns them that no matter how brave they are, he has seen Anubis' fleet, and one Tel'tak is no match for a massive fleet. Bra'tac however, tells him that they will use the ship to find something far more powerful than whatever Anubis can throw at them. Ronan agrees and has only one condition: that he join them to find the means to defeat Anubis. Teal'c and Bra'tac accept his offer.

Carter, Jackson and O'Neill are ready to step through the Stargate to Chulak with O'Neill's supplies. Before they set off, Weir tells them a bad joke, though O'Neill says there is still hope for her to become better. A while later, they meet up with Teal'c, Bra'tac and Ronan, and set off in his cargo ship. On the way to Proclarush, Carter and Jackson check up on O'Neill, who admits to feeling "fron-aches". When he hears that even at top speed, the Tel'tak will arrive in two days, O'Neill feels this is too slow, and gets up to work on making the hyperdrive faster.

Meanwhile, three of Anubis' Ha'tak vessels exit hyperspace over Earth's Moon and are slowly making their way to Earth. The ships are detected by the military. In the White House, President Henry Hayes, Vice President Robert Kinsey, Major General George S. Hammond, General Francis Maynard and General John P. Jumper, the Chief of Staff, decide on what action to take. Hammond suggests that only three ships out of dozens have arrived because they are going to goad Earth into revealing their defenses. Hammond suggests holding off the Prometheus, as this could mean that the Tau'ri have successfully bluffed about their defensive power. Hayes decides to remain at DEFCON-3, and make contact with the governments of Canada, China, France, Russia and the United Kingdom to let them know what Earth is facing ahead.

Aboard the Tel'tak, O'Neill has reconfigured the ship's Control crystals; he asks for Carter's Zat'nik'tel, and fires it at the crystals. This action causes the ship's hyperdrive to increase in speed. Carter then tells O'Neill that Hammond authorized her to command the team should O'Neill's brain be overwhelmed by the Ancient knowledge. Given the circumstances, O'Neill immediately tells her to take command and resigns from his post. Carter, having missed an opportunity in Jack's home, attempts to convey her feelings, but O'Neill cuts her short, claiming he already knows what she would say. Later, the Tel'tak arrives at their destination and drops out of hyperspace.

What they see when they arrive is not what they expect. They discover that the planet's sun has turned into a Red giant; one million years ago, the planet was probably much like Earth, but the red giant has caused the planet to be covered in molten rock and lava. They have arrived far too late. However, they notice that O'Neill packed the Hazmat suits, so subconsciously, he knew the planet was dead. Because Carter is now in charge, she orders him to scan the planet's surface to look for any sign of a man-made structure in the area. He - fairly quickly - finds a cavernous dome underground, caused by some sort of shield or force field protecting the area, though it doesn't seem to be big enough to contain a city. They decide to check out the area.

In Anubis' mothership, Anubis' First Prime, Her'ak receives communication from the advance invasion squadrons over Earth; there is no sign that they are being challenged. Anubis orders them to begin and the three Ha'taks launch an attack. Later, in the White House, Maynard informs the President that they contacted the captain of the destroyer USS Spruance, who reported that the aircraft carrier USS Nimitz had been destroyed, along with a cruiser in her battle group, before communications were lost.

Back over Proclarush, the Tel'tak positions itself over the dome. In Hazmat suits, SG-1 is ringed into the outpost. They keep in contact with Ronan and Bra'tac. Carter finds high levels of radiation, and the rings may have compromised the dome's structural integrity. They can't stay too long. The facility is dark, but O'Neill still manages to find a throne-like chair. There, he proceeds to sit down and places his hands on the armrest controls. He erects a forcefield, and takes off his Hazmat hood. Carter reads a stable and breathable atmosphere, so the team also take off their hoods. He then activates a holographic map of the Milky Way which zooms into our solar system, and Earth, as it was 30 million years ago before continental drift. They wonder why O'Neill is showing them this. His reply is "Terra Atlantus", "Terra" meaning Earth, and "Atlantus" referring to Atlantis, the name of the Lost City.

The team comes to the conclusion that the city they have been looking for the past year has been on Earth all along, and they have to travel all the way back. O'Neill, who is now only able to speak very little, tells them there is something they need. He puts his hood back on, as does the team. He activates a panel on the floor, which raises to reveal a glowing power source. Once he removes it, the structure starts to collapse. The team quickly runs to the ring platform and signal Bra'tac to ring them back aboard.

However, as he gets up, Bra'tac is betrayed by Ronan, who stabs him in the symbiote pouch. He reveals himself to be an agent of Anubis, and calls Bra'tac the betrayer of the "one true god". As Bra'tac falls to his knees, he tells Ronan he should have stabbed him in his heart, as he no longer has a symbiote. He still has enough strength to fight back, and during the brief struggle, tells Ronan that he may be younger, but not wiser. Bra'tac manages to kill Ronan and with the last of his strength, he activates the rings, and SG-1 is transported aboard before the structure on the outpost collapses. They tend to Bra'tac and O'Neill stretches out his arms over his wound, and reveals himself to have healing powers. Bra'tac declares that once again, he is in O'Neill's debt. Teal'c then plots a course for Earth.

In the Oval Office, the President and the advisers further discuss what to do, when the power goes out. Anubis unexpectedly appears in front of them. The Secret Service team responds by firing at him, but the bullets merely pass through him, revealing that he is merely a hologram. Hayes talks to the hologram and Anubis demands Earth's surrender. Hayes attempts to bluff Anubis out of attacking by telling him that Earth will give him a good fight; he asks for Anubis' surrender instead. After the hologram leaves, more than 30 additional ships exit hyperspace over Earth. The ships don't attack Earth, but proceed to take out power grids around the World. Kinsey suggests a team go to the Alpha Site as a contingency plan, though in the end, Kinsey is the only one who goes as the rest want to stay and fight. Hammond also wishes to stay, so Hayes offers him another assignment: They decide to launch the Prometheus, and Hammond is to command it.

In hyperspace aboard the Tel'tak, O'Neill works on the ring transporter platform. Teal'c visits O'Neill and wonders if he is making some kind of weapon using the transporter. However, O'Neill doesn't answer because his speech has mostly been overwritten by the Ancient knowledge. When Teal'c is about to say something else, O'Neill stops him knowingly. Teal'c leaves him to continue working.

Kinsey is in the Embarkation room about to head through the Stargate to the Alpha Site. Weir brands him a coward, though he claims he's doing this for the survival of humanity and announces he will be done with her, should she survive. Suddenly, the power goes out, shutting down the Stargate. Weir orders the iris closed using the manual iris control over Kinsey's objections. Seconds later, an active wormhole dials in and a massive explosion rocks the Gate Room, possibly from a naquadah enhanced weapon. Colonel Stewart Pearson then receives an encoded message from SG-1 that they are not coming through the Stargate, which prompts both Weir and a very reluctant Kinsey to call the President.

On the phone, Weir suggests that the Prometheus be used to buy SG-1 time to get to Atlantis in Antarctica. However, Kinsey refuses to let this happen. After arguing, Hayes tells Kinsey to "Shut the hell up!" He then forces Kinsey to resign, stating that after he read information given to him by Richard Woolsey a few weeks ago, he has enough info to have him shot. After Kinsey leaves in disgust, Hayes allows Weir to continue and agrees with her advice. Meanwhile, Hammond arrives aboard the bridge of the Prometheus and the crew prepares to take off.

Aboard the Tel'tak, Jackson interprets O'Neill's actions. He is modifying the ring transporter's matter stream transmitter to bore a hole through the ice. With Anubis' fleet over Earth, they decide to drop out of hyperspace dangerously close to the planet's surface. They do so, and the ship plummets toward the arctic surface, though fortunately, Teal'c manages to regain control of the ship, and he levels off over a plateau. O'Neill proceeds to use the modified ring transporter and burns a hole through the ice. However, it will take some time and Anubis has detected the ship. He sends a wave of ships to destroy it. Bra'tac detects several Al'kesh and Death Gliders heading their way and also notices more ships coming from the opposite direction, but they aren't Goa'uld.

The other ships are revealed to be F-302 fighter-interceptors, who start attacking the Al'kesh and Gliders. The 302s are followed by the Prometheus, from which Hammond orders the Tel'tak protected at all costs. However, the 302s quickly expended their weaponry, so Hammond orders them to divert to McMurdo Air Force Base. Fortunately, Prometheus buys enough time for SG-1 to ring below the ice. Anubis' mothership establishes a weapons lock on Prometheus and starts firing. With shields rapidly failing, Hammond sets a course and orders the Prometheus to engage Anubis' ship.

SG-1 investigates the "city," which looks similar to Taonas. They find a chamber, which O'Neill describes "dormata", Ancient for "sleep". They then hear a noise and investigate. There, they find Anubis, who tells the team they have failed. However, O'Neill realizes immediately that he is only a hologram, and passes him. He finds a chair like the one on Proclarush and opens a similar panel with a burned out power source. He replaces it with the one previously found. Just then, the rings activate, revealing two Kull warriors. While Carter, Jackson and Teal'c hold them off, O'Neill sits in the chair. While a Kull warrior is killed, two more arrive. The Prometheus nears Anubis' mothership, but shields are down, and the ship won't last much longer. Hammond orders a collision course.

O'Neill activates the chair, where by using his mind, is able to open a hole on the ground. Hundreds, even thousands, of yellow energy projectiles erupt from the floor, wiping out the Kull warriors. They fly to the surface and destroy all the Gliders and Al'kesh in the enemy wing, ignoring Bra'tac and the Tel'tak. They continue on towards Anubis' fleet, leaving the Prometheus untouched. Hammond orders the ship to break off the attack, while the drones go through Anubis' shield with no effort whatsoever. While watching his fleet destroyed, Anubis roars and holds his hand in front of his face as his ship blows apart.

Back in the ice cave, O'Neill, drained to exhaustion, indicates that he needs to go into the chamber he pointed out earlier. The chamber activates, freezing O'Neill into suspended animation as he says, "Aveo ... amacus," Ancient for "good-bye, friends." Carter, nearly in tears, is convinced a way to save him is here, but to Daniel, it is now obvious that this base, like the outpost on the molten planet, is not the Lost City. As Teal'c wonders aloud where Atlantis really is, SG-1 can do nothing but stand and look at O'Neill, frozen in time.