Renee Rienne steals a chemical from an army storage depot in Frankfurt while Jack meets Sloane in a restaurant. Sloane asks to be reinstated in APO so he can find a cure for Nadia, Jack says he's already made the request but a senator is blocking the request.

In Marseilles, Rienne administers the chemical to a man who's been cryogenically frozen. At the APO office, Dixon reports that the chemical is Atropine ZX, an experimental substance used to resuscitate gravely injured soldiers. The thief, who he's identified as Rienne by way of video footage, had also stolen the frozen body from DSR. As Syd volunteers to speak to her, Jack privately asks Tom to keep an eye on Renee.

Syd and Tom meet Renee in Marseilles and return to her loft, where the now revived but disoriented man surprises them. He holds a knife to Renee's throat. They realise that the man is Luc Goursaud, Renee's father, and calm him down. Luc reveals that it was Aldo Desantis who had frozen him. Before he can speak about Prophet Five, Luc has a seizure and slips into unconsciousness.

Gordon Dean approaches Sloane and reveals the identity of Senator Lewis, who is refusing his reinstatement. At Dean's suggestion, Sloane wins his reinstatement by threatening the senator's child.

Jack gives Tom and Syd the name of a doctor they could bring Luc to. Overhearing the name "Desantis," Rachel remembers that, while working for Dean, she had stored files on Desantis in a San Francisco facility.

Mercenaries converge on Renee's loft and pump gas into the vents. Tom makes his way out and plants a bomb in their van. In a flashback, Renee recalls that her father had once worked for Desantis, but they had become enemies.

Meanwhile, Dixon and Rachel go to the San Francisco facility and ask to be shown a storeroom, where they leave a case. Marshall's latest invention crawls out of the case: a spider robot with a topographic camera. Marshall controls the device from a remote location, directing the spider to find and scan Desantis' files. Later, they learn that the documents detailed the manipulation of genetic and neural pathways. They also discover that the brain scans of Luc Goursaud and the man in the cryogenic chamber were not the same.

Tom returns to the loft and finds a beacon in Luc's cryogenic chamber. He and Renee use the beacon to alert APO. Syd learns about the beacon through Luc and iscovers that he had guided the mercenaries to the loft. His cover blown, Luc takes Syd hostage. When Renee and Tom return, they realise that Luc is not Renee's father. Suddenly, the building is blown apart and a helicopter picks up Luc.

Later, in a North Korea hospital, Gordon Dean meets man formerly known as Luc, referring to him as "Doctor Desantis." Desantis reports that the "woman" is now calling herself "Renee Rienne" and that she's working with the CIA. Dean assures Desantis that keeping an eye on her won't be a problem.

Sloane, his clearance granted, walks down the halls of the APO office.

"Out Of The Box" first aired in America on October 27th, 2005.
This episode marks Jesse Alexander's eleventh written episode and also Jay Torres' first directed episode of Alias.
The location of the lobby during the Marseilles mission is actually the same one that was used in "And So It Begins" and "A Dark Turn".
There are no 47 references.
Location ciphers: Marseilles and San Francisco.

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