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Carter leads SG-5 to investigate a planet which has signs of either an Ori singularity or a black hole developing. Oddly, the planet they are trying to travel to has a protective device on its stargate: if anything organic tries to travel to the planet without the correct authorization, the incoming objects are sent to another stargate. Carter quickly figures out how to get around the device, and they again head to the planet, with the rest of SG-1.
They discover an underground science lab, with controls and data written in Ancient. Inside the lab, they find evidence of genetic experiments (including a DNA-alteration device, as seen used by Nirrti in season 6's "Metamorphosis") and a man in stasis. Mitchell inadvertently revives the man, and they return him to the SGC while Daniel continues to study the lab.
The man, whose name is Khalek, claims that he was abducted and experimented upon in the lab. He asks to return to his home planet. He appears to be weak and guileless. Back in the science lab, Daniel discovers in the data logs that Khalek is a Goa'uld-human hybrid developed by Anubis; Khalek contains Anubis's DNA and would have access to the Goa'uld genetic memory of Anubis's past, as well as Anubis's predecessors.
Daniel returns to the SGC with this information and Khalek is immediately restrained. When Daniel begins to interrogate him, Khalek tries his victim routine, but once Daniel reveals that he knows what Khalek is, Khalek goes into a chilling monologue about the pleasure Anubis felt in killing and how much he wants to get the chance to feel this pleasure. Obviously, Khalek is not a good guy.
Landry, Dr. Lam, and SG-1 confer about what to do with Khalek. He is obviously some type of advanced human being, possibly similar in physiology and abilities to the Priors, so there is some potential in studying him, if it can be done safely. They speculate about returning Khalek to stasis, either on the other planet or in the base in Antarctica. Shockingly, Daniel recommends killing Khalek immediately. He does not believe Khalek can be completely restrained, and that if he develops his abilities any further, he might be able to ascend and become Anubis II.
Before Landry can decide what to do, Mr. Woolsey arrives on behalf of the international committee now overseeing the SGC (in return for funding, as was necessitated by "The Ties That Bind"); the international committee wants Khalek to be kept alive and awake for study. If Landry doesn't cooperate, Woolsey threatens to have him removed from command.
The studying begins, over Landry's protests. One of Anubis's monitoring devices from the planet is used to gauge Khalek's development. Most humans use 5 - 10% of their brain capacity; Khalek is already using almost 70%. From Anubis's records, approximately 90% is needed to consciously ascend, which is presumably Khalek's goal. Khalek demonstrates that he already has some telekinetic capability by destroying equipment in the room, freeing himself, and trying to escape. Mitchell shoots him in the chest twice with a pistol; Khalek survives and heals himself at an amazing rate.
The studying begins again, with increased security precautions. The floor around Khalek's restraining chair has 50,000 V flowing through it. The doorway has a one-way forcefield. Dr. Lam has installed a shunt to drug him quickly with a dopamine inhibitor, which should dampen his special abilities. Khalek reveals his telepathic abilities by taunting Woolsey; unseen by his captors, he also disables the drug shunt. During this phase, Mitchell is personally overseeing the guarding of Khalek. Meanwhile, Daniel, Carter, and Teal'c are trying to uncover more information from Anubis's lab.
Landry finally decides to put Khalek back into stasis on the other planet, regardless of the consequences to his command or the SGC budget. Mitchell oversees the slow and careful transport of Khalek to the stargate. Just then, the rest of SG-1 returns and informs Landry that Khalek needs more treatments with Anubis's devices before he will be able to ascend, so Khalek probably wants to go back to the lab. Landry cancels the transport order, but Khalek is aware of their plans and escapes.
Khalek leads the SGC on a merry chase through the facility, wounding and killing many personnel on the way to the stargate. He is essentially invulnerable, as he can stop bullets in their tracks telekinetically. He takes control of the gate computer and dials the gate for the planet with Anubis's lab. However, he was unaware of the gate-protection program, which Carter altered to have the incoming person just sent back to the SGC. When he returns to the SGC, he blocks Mitchell's pistol shots, but somehow doesn't notice Daniel, whose shot is successful. At the end of the episode, Woolsey apologizes to Daniel for not believing him about the threat Khalek posed.
This episode was much more interesting than almost anything else this season. Khalek was a riveting character to watch. His transformation from his innocent victim act to his true self was astonishing. He truly seemed like evil personified. His taunting of Mitchell and Woolsey fit right into his character. Somehow everyone except Woolsey knew that keeping Khalek alive was a horrible idea and the sense of impending doom hanging over the episode was palpable. Khalek certainly got the chance to enjoy killing humans; during the chase scenes he initially just threw his attackers against the wall, but in the end, it appears that he had the SGC airmen turn their guns on each other, just for fun.
We knew right away that Khalek presented a serious threat, since Daniel was the one who first advocated killing him. Daniel certainly has the most first-hand experience with what ascending beings are capable of and what Anubis's abilities were, so he knew just what kind of threat Khalek was. What would have happened if Khalek had ascended? The other ascended beings would not have let him interfere with the affairs of corporeal beings. Would they have tried to return him like they did Anubis? How could Khalek be sure that they would fail and he wouldn't just be a normal human? I suppose since he had Anubis's knowledge, he would've known Anubis's trick to remain part-ascended.
Why did Anubis create Khalek? It's speculated that he was trying to create better servants and warriors for himself - apparently the Kull soldiers not being sufficient. Since Khalek has Anubis's memories of Daniel, we know that his creation must have been relatively recent. Was Anubis trying to create a better "host" for his half-ascended being to inhabit? We know that Anubis has been interested in advanced human physiology as long ago as his interrogation and study of Jonas Quinn in season 7's "Homecoming". We're still not sure why.
Woolsey makes his first appearance this season, working on behalf of the international committee governing Atlantis and now also the SGC. Although he chose the worst course of action here, he certainly wasn't being illogical or unreasonable. Without Daniel's dire warning, certainly the SGC would also have been in favor of studying Khalek. Woolsey makes the very good point that even with the threat of the Ori and their Priors staring the SGC in the face, the SGC has made no progress toward defeating them. However, I do think that Woolsey stuck to his decision for a bit too long; after the first revelation of Khalek's telepathic abilities, I would've thought Woolsey would realize that any hope to contain Khalek were doomed. But Woolsey redeemed himself to me with a very sincere apology in the end with no excuses.
I don't have many more comments about the episode. I found it a little odd that only Mitchell stuck around to supervise Khalek during some of his interrogation, but that the rest of SG-1 returned to the science lab. I suppose they were probably doing more good there, it just felt odd for them to not be at the focus of the action.
At the end of the episode originally, I was wondering why Khalek hadn't read Carter's mind to know that he would be "bounced back" from the other planet through the stargate. However, thinking back, I realized that Carter was never in close proximity to Khalek after she set that up - that's some nice writing. Presumably Khalek has to be relatively close to someone to read their minds, possibly on a line-of-sight.
Where will the SGC go from here? While they don't have Khalek alive to study, they have his body, plus all of Anubis's equipment in the lab. What use will they make of these things? Maybe Woolsey's hope of a weapon to fight the Ori will be realized.