The scene is a huge pyramid on a grey, barren-looking world. SG-1 is gathered in the Control Room watching the telemetry sent by the MALP: the pyramid is at least a thousand meters high and Mayan, but much larger than anything found on Earth; in fact, all pyramids on our planet could fit inside and there would still be room left over. Carter detects a substance called leptons that can stop neutrinos, which normally pass through anything, no matter how dense. Jackson, too, finds something of interest - on the far side of a narrow stone bridge there is a pink crystal skull, identical to one found by his grandfather in Belize in 1971.

The skull, Jackson explains, is unique because no one could explain how it was carved from a single crystal against the grain given the technology of the time. According to Nick Ballard, Jackson's grandfather, the skull possessed certain abilities; he claimed that he was transported to see giant aliens after gazing directly into the skull's eyes. Nick was laughed out of the archaeological community because he wasn't able to substantiate his claim - he wasn't able to make the skull work again - but O'Neill and Carter both point out that no one believed Jackson's theories that Earth's pyramids were actually landing sites for alien spaceships and he was right.

SG-1 visits the cavern but is restricted to ten to fifteen minutes because of the neuon radiation. Crossing the narrow stone bridge to the platform where the skull rests, Jackson gazes directly into its eyes. As the skull begins to glow the radiation spikes 300%, then 400%, and an energy field is emitted. The energy dissipates after Teal'c shoots the skull with a zat gun, but suddenly the team members can no longer see Jackson. Teal'c walks up to the platform - and right through an unconscious Jackson, lying prone on the stone floor. Carter shouts that the radiation levels are off the scale just before she faints; O'Neill catches her and begins racing for the Stargate as he yells for Teal'c to follow. Arriving back on Earth, the three collapse on the ramp.

In the infirmary, O'Neill wakes and reports to Hammond, while Teal'c is already almost healed thanks to his symbiote and Carter is still unconscious. O'Neill's hypothalamus was affected by the radiation and his respiration, internal thermostat, and heartbeat are all fluctuating, but eventually he (and Carter) will recover.

From the Control Room, Hammond uses infrared sensors via the MALP to try to locate Jackson but there's no sign of him. Teal'c arrives and asks to go retrieve the crystal skull, to which Hammond agrees. As Teal'c is putting the skull in a bright yellow case, Jackson awakes, and Teal'c runs right through him as if he weren't there as he leaves. The archaeologist calls his name and Teal'c stops, looking around as if he'd heard, but sees nothing. Disconcerted and not knowing what's going on, Jackson follows Teal'c back through the Stargate where the Jaffa reports to Hammond that there was no sign of Dr. Jackson. No one else in the Gate Room can see Jackson either. Hammond tells Siler to get the skull to Dr. Rothman and Teal'c points out that Carter will also want to see it - and she will, Hammond says, as soon as she recovers. Jackson, wanting to know what she needs to recover from, follows Teal'c to the infirmary where Carter has yet to wake up but O'Neill feels ready to leave, despite Fraiser's assertions that he has to stay. The colonel tries to get up but collapses on the floor, leaving Teal'c to put him back on the bed.

Dr. Rothman is skeptical about the skull's reputed abilities to transport Jackson to another place, but Hammond merely orders him to study it: he wants a report in twenty-four hours. As he leaves, Teal'c warns Rothman not to look the skull directly in the eyes.

Teal'c is meditating in his quarters when Jackson thanks him for coming back, otherwise he would likely have been stuck on P7X 377. Suddenly Teal'c opens his eyes and asks if there's anyone there; he then gets up and checks at the door, walking through Jackson again. The Jaffa can somehow sense Jackson's presence, but is unable to see him.

Rothman is staring the skull directly in the eyes when Carter comes in and yells at him to stop. He was trying to prove a point, he says: that the skull isn't responsible for Jackson's disappearance, much as he would like it to be so that they could retrieve him. The two argue over the validity of the skull being able to transport someone away and Carter takes over the testing. It's at this point, when Carter takes a drink of water, that Jackson suddenly wonders why he isn't hungry or thirsty. Could he be dead? Just as he says this, Carter gets a shiver. Fraiser says it's because her hypothalamus still isn't working properly, but Jackson thinks it was because of him, because he's a ghost.

Back in the Control Room, Carter reports her inability to find anything useful to Hammond just as they're about to launch a UAV for a long-distance search for Jackson. When the general refuses to let any more team members go back to P7X 377 without proof that Jackson is actually there, Carter suggests looking for Nick: if the skull is responsible for Jackson's disappearance, then maybe his grandfather will have some idea of where to look. Fraiser announces that she's done some research on Nickolas Ballard and that his current address is a psychiatric facility in Oregon; apparently the stress of not being believed caused a mental breakdown and he checked himself in voluntarily. He and Jackson had a fight four years earlier and hadn't spoken since, but any friends of Jackson's would be welcome. Hammond agrees to let SG-1 speak to the man, but the details have to be kept secret since the Stargate programme is classified.

At the psychiatric facility, Jackson goes in ahead of the others to tell his grandfather to share all that he knows with his friends. When the other three members of SG-1 arrive, Nick refuses to share any information unless he can see the new skull. O'Neill manages to convince Hammond to okay it: since Nick is in a mental hospital, who would believe him even if he did tell anyone? O'Neill leaves Hammond's office and the general receives a phone call from his granddaughter Kayla, who wants him to attend her school play the following evening. Sadly, he might have to miss it because "a very close friend of mine is missing."

Having been brought to the SGC, Nick looks at the skull and perfectly describes the cavern in which it was found. After he'd been returned he'd searched for the cavern again but could never find it, but he believed that it was nowhere on Earth. He'd been surrounded by an energy field and taken to see the giant aliens, who had spoken to him in Mayan: "The enemy of my enemy is my friend."

As O'Neill walks Carter to the elevators, she reveals that she gets the feeling that Jackson's still around, but dismisses it as being due to missing her friend; O'Neill offers that it may be radiation sickness. Unseen to both of them, Jackson is there.

Nick is taken to VIP quarters, where he begins to apologize to Jackson for not taking him in when his parents died. Then he turns and looks directly at Jackson: he had been able to see his grandson the entire time but had dismissed it as a hallucination. Jackson assures him that he's real and that the skull did something to him: he was in another dimension or out of phase. At Jackson's insistence, Nick goes to see O'Neill and Hammond. Initially they don't believe him; when Nick says that Jackson is standing right beside him and O'Neill replies that he's lost weight, Nick - repeating Jackson's response - says "Jack, don't be an ass," to which O'Neill replies, "Daniel?" Jackson then says - through Nick - that they have to return the skull and let it finish what is started; the zat blast interrupted the process. Nick is the only one able to see him because he went through the same thing. Hammond is still a bit skeptical until Nick tells him that if they hurry, the general still might be able to make his granddaughter's play. This convinces Hammond, because he'd been alone when he'd taken that call, and he okays their return to the planet.

Nick goes with SG-1 and finds the cavern to be just as he remembered it. The crystal skull is replaced and Jackson looks into its eyes, triggering the energy field as the radiation begins to spike once more. As the field fades all of the others are able to see Jackson except for Teal'c, who can now see none of them. Carter theorizes that they must also be out of phase. Teal'c reports to Hammond that he can't see them and is ordered back to the base; after he leaves a giant alien appears as if from nowhere, hovering in the air and speaking in Mayan: "The enemy of my enemy is my friend." Jackson figures out that Teal'c wasn't affected because of his symbiote and tells the alien that they are also enemies of the Goa'uld. The alien says that they are welcome here. He chooses Nick to stay to exchange information and culture because he remembers the man from his first visit so many years ago. Jackson wishes Nick didn't have to stay, since they'd just started speaking again after four years, but Nick tells him that he has to. He tells Jackson that he's proud of him, and Jackson says goodbye to his grandpa.

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