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Once Jonas realizes what has happened, he piles even more guilt on himself. After all, he joined SG-1 to try to defend his world, not to lead the most dangerous villain in the galaxy right to it. Of course, how could he ever have foreseen his capture and "interrogation" by a method he could not possibly fight against?
Once Anubis arrives at Jonas's homeworld, he takes over the capital city of Kelowna. After some public executions, the Kelownans relinquish their entire supply of naquadria. Anubis's subordinate Goa'uld go to work trying to harness the power of the naquadria and avoid the problems of its instability.
The Kelownans have hidden their stargate, and they use it to call Earth and ask the SGC for help. O'Neill and Carter travel to Kelowna to assess the situation. They also find out what Kelowna has been up to since their last encounter with Earth in season 6's "Shadow Play": just as O'Neill predicted, they used the naquadria bomb against their rival nations. We don't find out for sure, but we get the impression it wiped out a populous city or other similar target. The Kelownans claim it was the only way to get their enemies to negotiate a peace, which they did. We can see O'Neill and Carter's regret and I-told-you-so thoughts about these events: one wonders if the Asgard or Tollan have thought about Earth humans in that way! At any rate, the SGC has decided to try to help the people of Jonas's planet repel Anubis.
Meanwhile, Teal'c has been having a heart-to-heart talk with Lord Yu's first prime. The first prime admits that Yu has been erratic and forgetful, presumably because of his extreme old age. He can no longer be fully restored in the sarcophagus. Even so, the first prime will not directly go against Yu's orders. Teal'c convinces him to act for Yu (without consulting him, presumably so the first prime doesn't have to go against orders) in order to save face for Yu. Together they speak to Baal and convince Baal to take over the System Lords' fleet and defeat Anubis.
Teal'c travels to Kelowna to join SG-1 and inform them of the new plan with Baal. The SGC sends weapons, supplies, and two more SG teams to help Kelowna.
One of the interesting aspects of the scenes on Kelowna is O'Neill's attitude. He obviously has very little respect for the Kelownans, for a number of (good) reasons: they denied their responsibility for Daniel's death, they basically disowned Jonas (whom O'Neill has finally come to respect), and they acted irresponsibly regarding the naquadria bomb. Because of this, he can barely give the Kelownans the time of day. He delegates the actual interactions with the Kelownans to Carter and Teal'c (once he arrives). He does realize that the planet as a whole shouldn't be left to Anubis just because their leaders are stupid, but he can't hide his lack of respect.
Anubis's Goa'uld scientist accidentally causes an explosion on Anubis's ship while testing the use of naquadria to power the ship's weapons. During the power fluctuations, Jonas is able to escape from his cell and join Daniel. They decide to leave the ship via the rings, because Jonas remembered that one of the artifacts the Kelownans found was a ring transporter.
Incidentally, we find out that Anubis, like Nirrti, is interested in Jonas's physiology. While this is nice continuity, why would Anubis care? Nirrti wanted to improve her future hosts, but since Anubis is not corporeal, he doesn't need a host. Although we will see later in the season that he's interested in super-troops, so maybe he had Jonas in mind for that.
Meanwhile, Anubis begins searching the city for a crystal containing the notes on the naquadria research done by the Goa'uld that occupied the planet thousands of years ago. Carter realizes this, and fortunately the Kelownan officials know where the crystal is stored. Carter, Teal'c, and one of the Kelownan officials go to recover the crystal. They are captured by Anubis's Jaffa. Of course, they are conveniently in the same storage room where the ring transporter is, so Jonas and Daniel ring in, creating enough distraction for the good guys to overcome the Jaffa.
An interesting side point: I do not recall any of the Kelownans recognizing Daniel or expressing surprise that he is alive. There could be many reasons for this: the officials and other natives that see Daniel in this episode may not have been around during the events of season 5's "Meridian" when Daniel suffered radiation poisoning in Kelowna; even if they were around, it's been over a year and they just may not recognize him; and current events are happening so quickly that they just don't have time to connect it.
SG-1 (sans O'Neill) returns to headquarters with the crystal. One of the Kelownan officials immediately betrays them, calling in Anubis's first prime, Herak, and giving him the crystal. With total lack of subtlety, Herak kills the official point-blank. I guess he decided he was in such a position of strength that he doesn't even have to pretend Anubis doesn't intend to enslave the people on the planet.
Baal finally arrives, leading the fleet of the System Lords. The weapons on Anubis's ship are still broken, so Anubis quickly abandons ship. His ship is destroyed, but he escapes. This reminded me again of Star Wars: A New Hope, where Darth Vader manages to escape the Death Star's destruction.
Baal's attack has caused enough chaos in the headquarters that SG-1 and the other Kelownans are able to fight off the Jaffa. Herak clearly has a backup plan, and dials up the stargate. Carter manages to keep him from taking the crystal with him. Jonas takes a staff blast aimed for Daniel. Has Jonas worked off his guilt yet?
After this, it appears the SGC may get a breather. Anubis is still around, but he clearly has had a major setback so he'll have to regroup. On Jonas's homeworld, the major nations have decided to try to unify their planet. It's not stated, but we are given the impression that their relations with Earth may be improved. Will the SGC have better access to naquadria now?
The Kelownan government (what's left of it) has asked Jonas to return and be their representative in the new initiative. Clearly, Jonas also feels like he would be keeping Daniel from his rightful place on SG-1 if he remained, so he decides to return to Kelowna. In his goodbye scene, he finally gets explicit approval from O'Neill: "You deserved it", presumably referring to why he chose Jonas for SG-1.
In the end, we are back to the original members of SG-1. Again, they have shaken up the balance of power in the galaxy. Anubis has had a major defeat, and the System Lords a victory. What effects will there be of Baal taking over in Yu's place? Is Yu now ineffective? How will the SGC capitalize on these events?