Kasuf has heard a voice. SG-1 returns to the desert planet of Abydos, where Daniel's father-in-law leads them out to a barren plain. He tells them that he saw a whirlwind come out of an active Stargate, and heard it speak the name of Sha're, Daniel's deceased wife.
The team sees an almost magical whirlwind arise suddenly. Daniel identifies himself to the storm, which disappears -- leaving the form of a young boy. He identifies himself as Shifu, the Harcesis child of Sha're and Apophis.
The child represents the key to defeating the Goa'uld. As the product of the forbidden union between two Goa'uld hosts, he contains all the genetic knowledge of the Goa'uld who fathered him -- but no symbiote. SG-1 takes the boy back to Earth, and Jackson begins to question him about his Goa'uld memories. Shifu wants to learn about his mother, and Jackson answers his questions as best as he can.
Shifu has spent the last year with Oma Desala, a highly advanced alien being who taught him to bury the genetic memories deep within his subconscious. They are too powerful, too evil to be overcome, she taught him. The only way to gain victory over that evil inside him is to deny the battle.
But Daniel wishes to learn the secrets of the Goa'uld -- so Shifu offers to teach him. He places his hand on Jackson's forehead, and a burst of light renders Daniel unconscious.
He awakens sometime later in the base infirmary. It is not long before Daniel discovers Shifu's gift: he has given him some of his Goa'uld memories. Jackson begins to take advantage of the knowledge, forming a top secret government project to create a network of dozens of weapons satellites. Once in Earth's orbit, the powerful system will provide a powerful defense against Goa'uld attack.
But the knowledge is changing Daniel, and his friends soon take notice. He has flashes of Goa'uld memory: Teal'c kneeling before him as First Prime of Apophis, Sam being tortured with a pain stick, striking Jack with a Goa'uld hand device, and even torturing Apophis himself. Jackson begins giving orders, and assigns himself as head of the new project.
One year and $160 billion later, the satellite network is almost ready for launch. Shifu has been living with Daniel in a posh mansion. There are servants and assistants to cater to him. Teal'c has died mysteriously. And Jackson has removed Carter from the new program,apparently because she figured out that his motives were not pure.
When Sam confronts Daniel in his home, he has her thrown into prison. Colonel O'Neill visits her, and is convinced that something isn't right with Dr. Jackson.
O'Neill visits his old friend on the day of the launch, and finds himself transported (via Goa'uld rings Daniel installed in his mansion) to a secret underground facility. From his command chair, Daniel can monitor and troubleshoot the system.
The launch is a success, but Russia, China, and the other world powers object to the United States' secret launch of a powerful weapons network. Jackson tests the system by destroying a Russian satellite, but the nation doesn't get the hint. Rather than consider sharing the technology with the rest of the world, Jackson seizes control of it away from the government and turns the powerful weapons on Moscow itself.
O'Neill has seen enough, and pulls a handgun on his friend, unloading several rounds. But Daniel has taken precautions, installing a Goa'uld force shield around his command chair. With Jack helpless (and his disloyalty exposed), Daniel destroys Moscow.
As the energy wave floods across the city, Daniel's eyes flutter open again. No time has passed, and he is back in the S.G.C. infirmary.
He has learned the lesson that Shifu wanted to teach him: the knowledge of the Goa'uld is too evil to be used -- even to fight them. The power of the Goa'uld is part of what corrupts them; and as Daniel has learned, absolute power corrupts absolutely.
He stops his teammates and the Tok'ra from extracting any information from Shifu (using the memory recall device and za'tarc detector seen in "Divide and Conquer"), telling them that they must let him leave. Only by releasing his burden -- to obtain the Harcesis' genetic knowledge of the Goa'uld -- can Daniel find his own way again.
Shifu is transformed into a being of pure energy, like Oma Desala herself. Thankful for the memories about Sha're that Daniel shared, he leaves through the Stargate.