Colonel Jack O'Neill travels back through the Stargate to Abydos in the hopes of making contact with archaeologist Daniel Jackson—and discovering why communication with the planet was abruptly lost. What secrets lie beneath the surface?
The Stargate program on Earth has been unable to contact Abydos for several weeks, and Dr. Murphy assumes that the Stargate on Abydos has been shut down from the other side. They bring in the new military advisor, Colonel Jonathan "Jack" O'Neil, in hope that he will have some answers. Dr. Murphy, Katerina, Commander Klaus, and Catherine Langford each brief Colonel O'Neil on the current political situation on Abydos. Last time they were in contact with Abydos, there were three separate factions: the first had embraced help from Earth, and was led by Daniel Jackson; the second blamed Earth for all their current problems and, led by a person named Rhantaa, wanted the StarGate shut down for good; and the third group, which includes Kasuf among its members, refuses to believe that Ra is dead, or at the very least expects to see the rise of a successor. The people at the StarGate program have become concerned that the current political situation is responsible for the lack of contact with Abydos. Dr. Murphy believes that he might be able to force the StarGate open for a brief period of time, but only long enough for a one-person jump. O'Neil is sent through to try to figure out what's wrong on Abydos. Upon arrival, O'Neil is confronted by Skaara and a group of armed Abydans, who attempt to take him under custody. Daniel Jackson arrives on the scene, and when O'Neil asks him what is going on. Dr. Jackson tells him that the Abydans blame him for their troubles, and that he must be placed under protective custody, and that he must stand trial for his "crimes." After O'Neil is imprisoned to await his trial, Dr. Jackson and his wife Sha'uri come to visit him and give him the answers O'Neil wants. Apparently, after the death of Ra, the Abydan people began speaking of ghosts from the underworld. Dr. Jackson had originally just thought that it was yet another superstition based on ancient Egyptian myths, until he was attacked by one himself. The "ghost" was actually an outlaw who had not been seen by the Abydan people for years, and was assumed to be dead. Afterwards, Daniel discovered that there was a whole group of these outlaws who were actually living underground, hiding from Ra. When they learned of Ra's death, they decided to take over the surface world. The three political factions of Abydos temporarily joined forces to increase their chances against the outlaws, but tensions are still running high. Dr. Jackson tells O'Neil that he himself shut off the StarGate, knowing that if it had been left active the Underworlders would have destroyed it. Leaving it intact still allowed a chance that someone from Earth could get through. The next day, O'Neil's trial is held, and he is charged with destroying the society on Abydos and for disturbing religious beliefs of the community. Daniel Jackson is able to clear his name before the Abydan people, and they are able to move on to the Underworlder problem. O'Neil discovers the entrance to the Underworlder base, and assembles a team of warriors from all three factions to attack it. The battle is fierce, but O'Neil manages to destroy several basins of oil kept near the Underworlder camp, which in turn ignites a gas deposit under the ground. The enemy camp is obliterated, and with the three Abydan factions united once more, and O'Neil returns to Earth.