On their first visit to a new planet, SG-1 finds it subject to totally destructive volcanic activity and saves ten natives, the Tollan, a far more technologically advanced society. Their leader Omoc isn't grateful, nor interested in such a primitive race as the earthlings or any of the 'even more primitive' planets which are prepared to host them. Only one Tollan, Narim, shows an active interest in life on earth, especially in captain Samantha Carter and the cat Schrodinger she gives him, explaining his planet was destroyed after the Tollan supplied an unlimited energy source to a primitive neighboring planet which abused it for a cataclysmic weapon. Meanwhile, the White House authorized NID colonel Maybourne to take charge over the Tollan for military purposes, exactly Omoc's nightmare.

While exploring a new planet, Teal'c is stung by a giant insect whose venom causes a terrifying transformation.

A climate control device is stolen from a planet and SG-1 is accused of the theft. They have to find it and restore it before the planet freezes. Then weather on Earth starts to unexpectedly change and the team believe that the device has been stolen by rogue NID agents. Will they find it in time and how did the NID travel off world?

An alien incursion takes control of the base.

Col. O'Neill is dismissed from the SGC for stealing alien technology, and is subsequently approached to participate in an even more covert Stargate operation.

The SGC learn that the Russians have a Stargate of their own and they need the Americans' help with their problems with it that are affecting them both.

General Hammond mysteriously retires from the SGC and a new general is brought in, who breaks up SG-1: Daniel and Sam are scientists, Teal'c is with SG-3 and O'Neill commands a new SG-1. O'Neill tries to convince Gen. Hammond to return, but he finds out that someone ordered Hammond to leave or they would hurt his grandchildren. While the others are occupying the new general, O'Neill tries to find out who that "someone" is. Thereto he must place his trust in the one person he hates most: Maybourne.

Carter gets kidnapped and taken to an abandoned hospital where two doctors work to study the remains of Jolinar. She finds out that they have a Goa'uld, taken from the Russians, which they are planning to put inside a man named Adrian Conrad to heal his sickness. They need Carter to tell them how to get the Goa'uld out after he's healed. O'Neill believes the government is involved with Carter's disappearance and contacts Maybourne. Together, with Daniel and Teal'c, they find Carter but also find out that the Goa'uld has escaped inside Conrad's body.

When Teal'c is trapped in the Stargate buffer, the team must juggle the technical challenges along with personal, interdepartmental and diplomatic rivalries to rescue him in time.

Former Colonel Harry Maybourne comes to Jack with a proposition: Jack gets him a presidential pardon and Harry shows them the advanced weapons cache that Simmons was trying to get to. They go through with the deal, but Harry attempts to double cross SG-1. He manages to get through the portal leading to the cache, but with one unexpected item, Jack. They find themselves in a field and Harry's zat is missing. Jack, however, still has his P-90. Harry reveals that they are not at a weapons cache, but rather a utopia. He meant to live out the rest of his life there and believes that there is no way back.

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.

SG-1 is sent to warn Harry Maybourne that the goa'uld System Lord Ares is coming to the planet where he was banished, and in the process they find what may be an Ancient time machine.