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While on personal leave on Earth, Sheppard and Ronon learn that scientists have engineered a human-form Replicator — who is now on the loose.

Kyle and Amanda’s relationship hits a period of uncertainty after she makes a surprise visit home, but is uncharacteristically cagey about the reason why. Meanwhile, Jesse loses her patience with Kyle when he keeps putting off her training sessions.

Walt and Jesse attempt to tie up loose ends. The desperate situation gets more complicated with the flip of a coin. Walt’s wife, Skyler, becomes suspicious of Walt’s strange behavior.

Colonel Sheppard and Dr. McKay must protect a child princess on a pilgrimage before she can become queen, and learn that she has dangerous enemies threatening her life.

Sammy reminds Lechero that Papo is dead and presses Lechero to kill Michael. Lechero replies that he also wants Michael dead, but he does not want an uprising in Sona. Mahone receives a picture of his son through the mail. Lechero, Michael, Mahone, Whistler and T-Bag inspect the hole in the tunnel and Michael requests a saw and hammer to support the tunnel. Sammy takes the over the reign of Sona with the pistol delivered by Augusto and other three gangsters and promises a box of bottles of rum for the inmate that kills Michael. T-Bag convinces Bellick to give the chicken foot to Sammy, promising him a spot on the escape team. When Bellick discovers that there is no more acetone, he unsuccessfully tries to call-off the fight. Meanwhile Lincoln and Sofia visits Osberto and buy a bomb. Sucre plants the bomb under the seat of Gretchen’s car but she unravels that, saying she found Maricruz tracking the US$ 25,000.00 check she gave to him. Sammy leaves the fighting with Bellick to chase Michael, who is locked behind the door in the tunnel with Mahone. Sammy beats Whistler, who was left behind, trying to get the combination of the door. Michael removes a wedge from the hole and the tunnel collapses over Sammy, burying him, while Lechero and Mahone kill the three other gangsters. Sofia finds a wallet hidden in Whistler’s bag.

It’s Career Week at school. As Kyle and Josh contemplate their respective futures, Jessi’s quest for acceptance clashes with Kyle’s need for anonymity. Meanwhile, Brian Taylor seeks parenting advice from Nicole.

When an unassuming high school chemistry teacher discovers he has a rare form of lung cancer, he decides to team up with a former student and create a top of the line crystal meth in a used RV, to provide for his family once he is gone.

An automated lockdown traps Atlantis personnel in various parts of the city, each of them hoping the others will come to their rescue.

Sona’s Commander General Zavala takes Michel and locks him in a “hot-box” in solitary confinement to be punished by law or by Panama’s sun. Meanwhile Agent Lang brings Mahone back to Sona and gives an amulet to him that belonged to her father. Michael decides to tell the truth to General Zavala and he brings Whistler, who is submitted to torture and gives the name of Gretchen Morgan. Meanwhile Lincoln is blindfolded by Gretchen and has one minute of conversation with L.J. T-Bag proposes Mahone to kill Sammy; in return he would supply drugs for free for him. Bellick is challenged for a fight and he uses acetone to defeat his opponent. Gretchen is arrested and tortured by General Zavala and she gives the location of L.J. However she manages to revert the situation and kills Zavala. Augusto gives a pistol to Sammy and tells him that it is time to make a move.

Believing Jessi is dead, Kyle returns to the Tragers and reveals the truth about Madacorp. He’s now determined to take down MadaCorp and destroy all the information they have on Zzyzx.