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- A Nebari group come aboard Moya and attempt to mind cleanse everyone using a drug. Pilot and Rygel are the only two who can resist the effects. Crichton also remains unaffected due to Scorpius' neural clone.
- While docked at Peirpont Drift, a cop recognizes Beka and Seamus and notes that they are wanted for various crimes, but for some reason does not arrest them. Meanwhile, Dylan tries to mediate a disagreement between the Than and an ally of the Free Trade Alliance.
- The crew of the Enterprise struggles to cope with a planet of imitative people who have modeled their society on 1920s gangsters.
- While attempting to get the Arazians to rejoin the Commonwealth, he is arrested for sedition and sentenced to life imprisonment. In prison, he is forced to defeat a Magog prisoner in battle to win his share of the food. He wins the respect of the woman who appears to be in charge and finds Romy caged. Meanwhile, the crew of the Andromeda is anxious to find their captain.
- The Tok'ra are forced to evacuate their newly established base under attack from the Goa'uld. They flee to the SGC's Alpha site. Tensions rise between the allied factions, the Free Jaffa, Tau'ri, and Tok'ra. Jacob and Selmak feel the end of the Tok'ra is near and Sam finds a Naquadah generator has been sabotaged to function as a bomb. Jack suspects the recently arrived Tok'ra and attempts to weed out the traitor.
- Captain Dylan Hunt attempts to drive the invaders from his ship. He manages to scare Gerentex off, but he leaves many of his employees behind. He takes the Maru and uses it to send the Andromeda, still without engine power, on a course back into the black hole. The remaining scavengers work with Dylan to regain engine control and break free from the gravity well. Once free, they regain control of the Maru from Gerentex and Dylan invites the survivors to join his crew and reestablish the Commonwealth.
- When a long lost love returns, Tyr disappears from the ship to protect her from an assassin.
- The return of Flavin sparks a conflict between two rival gangs over who gets his ship and the bounties within. Rhade and Harper play the two sides to make money off their enmity. Meanwhile Flavin leads Dylan on a journey to help him develop as a Paradine.
- With a new commander of the SGC comes a new leader of SG-1, Lt. Col. Cameron Mitchell, a former fighter pilot who flew an F-302 in the battle over Antarctica. However, he is deterred by the fact that all the other members of SG-1 are leaving for other ventures: Teal'c to manage the Jaffa Nation, Carter to Area 51 for alien R&D, and Dr. Jackson to Atlantis as an Ancient expert. Mitchell endeavors to keep the members of SG-1 for himself, but they are increasingly tough to convince.
- SG-1 investigates a planet that is said to be the home of the Warriors of Sodan, a legendary tribe of Jaffa said to have not served the Goa'uld in 5,000 years. In an encounter with the warriors, Mitchell deals a deadly blow to one of the Sodan and is captured and taken to their village. There he awaits a battle to the death as punishment for his crime.
- When SG-1, minus Carter, investigates a previously unexplored planet expecting to find themselves in a pyramid, they are astounded to find themselves in a museum. Finding a party occurring in the lobby, they decide to leave and make first contact later, but they find that the DHD is a replica and thus incapable of getting them home. They are discovered and believed to be rebels and are forced to take hostages to buy time for their escape.
- A Prior of the Ori has established an ever-growing forcefield on a Jaffa-controlled planet called Kalana. A minor Goa'uld named Nerus, who engineered the multiple Gate connections required for the defeat of the Replicators, comes to the SGC with information on the event and offers his help.
- When Daniel's Unas friend, Chaka, is captured by another world's slavers, SG-1 goes to that world to rescue him.
- With the death of Omoc, the subsequent sudden Tollan reconsideration of their tech embargo leads to SG-1 suspecting a government conspiracy.
- After being saved by a group of free female Jaffa, SG-1 is taken to the females' home world to meet their leader, Ishta. Ishta proposes an alliance between her all-female rebel group, Haktil, and the Tau'ri. The Tau'ri offer her Tretonin to supplant their practice of taking the symbiotes from defeated Jaffa in the service of the Goa'uld. However, since Tretonin has only had two test subjects, Teal'c and Bra'tac, they are cautious to spread it among their ranks.
- The women of Moya travel to a dead Leviathan to buy a sensor beacon for Moya which will allow her to appear to be a different ship. While there Aeryn and Sikozu spy on a secret meeting between the Peacekeepers and the Scarrans.
- The Sabra-Jaguar pride goes to war with the Drago-Kazov, pulling Dylan and the Andromeda along with them, as per the terms of the Commonwealth treaty. Harper receives a message from a friend on Earth pledging his support for driving the Drago-Kazov clan off of Earth. Harper attempts to get the crew of the Andromeda to head for Earth to liberate it, but Dylan refuses to take the Andromeda to Earth. Instead, Harper takes the Maru with Rommie in tow to help with the resistance.
- Harper has been captured by General Burma, a man who believes all technology to be evil. Dylan struggles with recovering Harper, evacuating all the remaining Seefran planets to Seefra One, a.k.a. Tarn-Vedra, and dealing with Trance. Dylan supposes that something may have happened to Trance while inside Methus-2, the artificial sun they fixed and the last place Trance seemed to be herself, and goes to investigate.
- Andromeda receives a distress call from a Commonwealth prison, experiencing a riot the likes of which they've never dealt with before. Rommie discovers a now-missing prisoner was not recorded in the logs, meaning they was a mole, and Dylan and the others go in search of them.
- Owner and CEO of Colson Industries declares in a press conference that there is alien life and that he has proof. SGC fails in its attempts to keep him quiet on the battle over the Antarctic. However, they are greatly surprised when the proof he shows the media are not his satellite images, but a living Asgard.
- Dylan and the Andromeda are ordered by the reformed High Guard to transport and protect a candidate for election to Second Triumvir in the New Commonwealth. To the crew's surprise the candidate is none other than Beka's "Uncle" Sid, a sneaky and sleazy "businessman" who used to work with her father. Both Beka and Dylan are concerned that Sid may become part of the ruling body of the New Commonwealth, but when they find Sid unconscious and bleeding in his office they are forced to protect him from his assailants.
- Tyr leaves the Andromeda while it is in dry-dock for repairs to seek out other survivors of his pride. Dylan and the rest of the crew remain to see off the newest Commonwealth battleship, the Resolution of Hector. The AI to be installed in the Hector was derived from Andromeda and the former AI of the Wrath of Achilles, who was destroyed in a prior mission. Matters become complicated when Romy leads a strike force to take control of the Resolution of Hector.
- The Andromeda gets caught in the middle of a battle between two Nietzschean prides, one of which is the Drago-Kazov. They manage to capture a hostile fighter from the unknown pride. He reveals that the Drago-Kazov believe that his pride has in its possession a legendary Nietzschean slip-scout, the Midnight's Voice, claimed to have mapped billions of transit points in the slipstream, as well as the slipstream itself. Dylan looks into the near-mythic tale of the Midnight's Voice while Tyr interrogates their Nietzschean captive.
- The beings from another universe reappear. They take Rommie and use her for their own plans. The crew goes on a mission to rescue Rommie.
- Andromeda investigates the site of a reported Nietzscheanattack on a Commonwealth battleship, but find no sign of any conflict having occurred.l. Dylan must deal with the Nietzscheans in order to uncover the truth of what happened in orbit.
- In need of supplies, Crichton lands his transport pod on a dying leviathan which is full of hungry cannibals and a scientist who has the ability to create clones.
- When an SG geological exploration mission runs into deadly conflict with an indigenous Unas clan, Daniel gets Chaka to help seek an accord with it.
- A contact within the Rand Protectorate comes to Earth with news that the Ori have given his people a superweapon to use against the Caledonian Federation in exchange for their conversion to Origin. SG-1 plans to turn the people from their newfound religion and destroy the superweapon.
- Bra'tac and Teal'c encounter a heavily armed enemy with shielding protecting him from Goa'uld weaponry who took out two Goa'uld personal guards. They barely manage to defeat him and bring him back to SGC for study, but this new threat poses a greater problem for the Tau'ri.
- The Tau'ri and Tok'ra have used their captured super-soldier to determine his planet of origin. With Daniel, Dr. Lee, and the Ancient device they found in the hands of Honduran kidnappers, SGC must find a way to retrieve them if they are to have any chance of defeating the newly encountered super-soldiers.
- Following the death of a Jaffa on Earth and the disappearance of a prominent businessman, SG-1 starts an investigation into what remains of the Trust and into the actions of the Jaffa Nation. They discover that Ba'al is hiding on Earth after losing his forces to the Jaffa and that the Jaffa are secretly attempting his capture.
- While returning to Andromeda with repair parts after the Magog attack, the Maru comes under attack and crashes on an ice-covered planet. On board Andromeda, only Trance, Rommie, and Harper remain, with Harper struggling to cope knowing there's Magog larvae living in his stomach
- A large asteroid is discovered on a collision course with Earth.
- A group of nomads on an alien planet find Daniel Jackson naked in the middle of ruins and take him in. Jonas translates the tablet Daniel said was important and discovers that it describes the last city the Ancients were building before the plague. He surmises that the list of addresses Jack put into the computer while storing the Ancient data were Ancient outposts in temporal order. Thus the last of the addresses should be the "City of the Lost". SG-1 visits the planet and happens upon the nomadic people, now inhabiting the ruins of the Ancient city. There they find Daniel, but discover his memory is gone. They must recover his memories in order to discover the secret to defeating Anubis.
- Jonas Quinn returns to the SGC to ask for assistance in saving his nation. He explains that the Naquadria was originally Naquadah and a Goa'uld named Thanos started a chain reaction to transform all of his planet's Naquadah into Naquadria. A large vein of Naquadah has just been affected and the Kelownan scientists believe that the transformation will cause this large a deposit to explode, taking their entire nation with it.
- During a solar storm, Dylan's forced to leave Beka and Harper planetside. When he manages to pick them up, he also picks up a creature which devours the Maru's electronics, They must find a way to stop the creatures before they do permanent damage to Andromeda.
- On a mission to observe a nebula, SG-1 finds a crashed ship and its three human survivors. They soon come under fire from an pair of aliens bearing the weapons of the survivors. They repel the attack, but one of the three is wounded. She is taken to the SGC for treatment while Sam attempts to repair the ship. Jack and Teal'c feel that there is more to the relationship between the aliens and these humans, and attempt to trap an alien.
- Ex-Vice President Kinsey comes to Jack informing him of the Trust's activities including what seems to be a plan for the Russians to reclaim the Stargate they lent to the United States. He decides to use Kinsey as their inside man with the Trust. Kinsey wears a wire for his meeting with the Trust to set up a meeting with a high-ranking Russian general. The plan goes south when the signals get jammed just as the Trust makes an astounding revelation to Kinsey and they beam out.
- During an engine cool down break from hyperspace travel the crew of the Prometheus, with Major Carter as an advisor, encounter a space craft of unknown configuration. They hail the ship to no avail; the unknown craft opens fire upon the Prometheus. Carter attempts to override the safety protocols on the hyperdrive to make a short jump into a gas cloud, but in the attempt is knocked unconscious. She awakes to find the ship devoid of all its crew and, as she tries to escape the gas cloud by herself, she begins to hallucinate.
- Talyn is swallowed by a boodong, leaving Stark and Rygel stranded in a transport pod.
- After Harper's attacked by a dying Perseid, he gains a level of intelligence much greater than usual. A bounty hunter arrives for the dead Perseid, and Dylan looks into why the Persed was wanted. Unable to sleep, Harper begins to speak in various foreign languages, repair the ship, and invent new gadgets. The bounty hunter returns - to recover the information the Perseid lost.
- The president has asked that a documentarian go to SGC to create a film about its operations. His arrival is unwelcome to most and he begins to clash with the base personnel. Nevertheless, he conducts his interviews with SG-1 and the scientists in the employ of SGC. Meanwhile, an off-world SG team finds the remains of an Ancient city.
- The documentarian still a thorn in their side, SGC encounters an unforeseen predicament. With half of SG-13 off-world engaging enemy Jaffa, SG teams 1, 5, and 7 go in as backup. In the midst of heavy fire, O'Neill takes a staff blast to the chest. Many deaths from the encounter hit SGC hard and Senator Kinsey orders a full investigation into the matter.
- Anubis's super weapon has been put out of commission, but Yu's fleet has been diverted to the other side of the galaxy by Yu himself, allowing Anubis to escape into hyperspace. Jonas has been captured by Anubis and Daniel is still aboard Anubis's ship, evading capture. Anubis uses the mind probe on Jonas, learns of Naquadria, and begins his attack on Kelowna. The Kelownans seek aid from the SGC. Jack and Sam arrive on Langara to discover that the Kelownans have given Anubis Naquadria in order to secure their safety. They communicate with Daniel who is attempting to free Jonas. Teal'c has convinced Yu's first prime to seek a new leader of the System Lords, Ba'al.
- Dylan attempts to rescue Tyr and Beka by taking the Maru back towards the tunnel, but is forced to abandon it due to a large field of debris being sucked into the tunnel. When he returns, Beka and Tyr appear on Andromeda for no apparent reason. Now that her crew has been reunited, the Andromeda attempts to break free from the gravitational pull of the tunnel. During the attempt, Beka tries to slip too early, causing the Andromeda to be pulled into the tunnel. Dylan quickly takes control of the helm and pulls the ship out, but Tyr and Beka both seem to be acting strangely.
- The newly inaugurated President of the United States is briefed by the Head of the Joint Chiefs of Staff on the Stargate program. Former Senator, now Vice President, Kinsey attempts to get his running mate to back his policies for the program, but the president decides to look into the situation himself. Kinsey gets Richard Woolsey to convince the president of his agenda.
- While the Andromeda is hosting a diplomatic conference, Harper encounters a reporter who is able to remove the Magog larvae from his guts. She offers to remove them all in exchange for the information Harper previously had downloaded into his brain. A high-ranking member of the Sabra-Jaguar pride arrives at the conference unannounced to join the Commonwealth.
- For Dylan's birthday surprise, Harper overrides some of Andromeda's protocols to spring a surprise party. Becca gives him a unique gift; the map to Tarn-Vedra, the Commonwealth capital of legend where Dylan was born There's anxiety amongst the crew as they prepare their journey.
- As the Goa'uld summit continues, Daniel finds himself face to face with Osiris. He fools him in the same fashion as he did with Yu, but cannot bring himself to cause the death of Sarah, Osiris's host. He remains to uncover information about the unknown master of Osiris. Lantash, having taken Lt. Elliot as a host, guides the rest of SG-1 in escaping the fallen Tok'ra base.
- While SG-1 is exploring a crashed alien ship full of passengers in cryostasis, an alien force downloads a number of their consciousnesses into Daniel.