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.

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 finds a Goa'uld-Human hybrid in stasis in an abandoned Goa'uld lab and take it back to Earth to study, where they learn it was created using Anubis' DNA.

SG-1 is tasked to accompany members of the International Oversight Advisory, including Richard Woolsey, on a tour of the Gamma site. The visitors are suitably impressed but everyone is put in danger when a carnivorous insect escapes from the lab. The base is locked down and no one is allowed to travel through the gate. The bug is linked to the Ori - it's appeared on several planets that they've visited - and Daniel thinks it may be their follow-up to the virus. SG-1 and the IOA visitors take refuge in a cave, but Gen. Landrey is left with little choice but to flood the planet with a deadly neurotoxin to destroy the bugs. SG-1 looks for away out before that happens.

As the Ori invasion continues, Vala and Daniel must deal with their leader, Vala's young daughter, who is rapidly aged by the Ori to serve their purposes.

The team goes off-world and ends up in serious trouble. Meanwhile, Landry is faced with having to decide whether or not Vala can be trusted to remain at the SGC.

Daniel Jackson, who was left behind fighting off Adria while the other SG-1 members escaped through the Stargate, is found working as a Prior: the best in the business, who doesn't need to use any threats to talk people into conversion to Origin. Hoping there is still some of his personality left, the team (plus General Jack O'Neill) kidnaps him. Daniel explains how he temporarily has Merlin's personality and knowledge in himself, and had deliberately allowed Adria to turn him into a Prior, while delaying to finish Merlin's weapon she'd wanted, meanwhile hoping to get an Ori ship for Earth's side. But time is running out, since the team took unexpectedly long to capture him. Still, the generals, Carter, and Vala are most reluctant to go along with releasing him and opening the wormhole he needs to bring the weapon through. Even the White House wants to kill him, or at best, keep him in stasis until he is reverted to his human nature by Merlin's genetic manipulation. But then his plan is wasted- unless the others can be trained to do it in his place (so only they are at risk, not the entire galaxy in case Daniel is Adria's Trojan Horse). After giving them the necessary information, Daniel suddenly frees himself while Richard Woolsey is with him and takes control of a space ship after beaming up Jack too, just after the others have undertaken their mission to Adria's lair, where Daniel, about to be genetically reverted, arrives just in time to tip the balance in their favor.