Eli's mom is sick, and Eli must rush home to see to her. Once on Earth, he realizes that she won't come out of her depression until she realizes that he's OK, and cares about her.
Eli's Earthly woes are matched on the ship. No one can figure out why Chloe, who's been acting strangely, has recovered so quickly from her gunshot wound, but when she goes missing and is found in a daze in one of the cargo holds, the crew realize that she must be under some kind of residual genetic manipulation program from her abduction by the aliens. Young wants to quarantine her immediately, but Rush, who has been making huge strides in learning how to control the systems of the ship, convinces him to let her go about her life, under careful observation. He uses her vulnerable state to get her to solve an equation for him - an equation that will give him even more control over Destiny - but he continues to keep the bulk of his knowledge a secret from the rest of the crew.
On Earth, Camille is reconnecting with Sharon, but the pressure of a cross-galaxy relationship is wearing on her, and domestic tensions only get higher when Camille rushes to Eli's side to counsel him through his crisis with his mother.
Young has decided to give the Lucian prisoners a trial integration with the rest of the crew, in exchange for the intel they've been providing, but he may have to rethink his decision when Simeon, one of the Lucians, gets inappropriate with Park. The man is locked up, and Varro attempts to patch things over - which has an effect on TJ, but the rivalry between Simeon and Greer has been ignited, and is not likely to cool down anytime soon.
Brody, Park and Young are all becoming suspicious of Rush who, in a bind, shows them the equation that Chloe solved, and implies that the erratic behavior of the ship - dropping out of FTL with no gates nearby, turning off course for no apparent reason - is a result of her sabotage, at which point Young proceeds with his original plan and has her quarantined.
Camille, who is unable to solve her own domestic problems, is at least able to help Eli: She orders immediate clearance for his mother, and allows her to use the communication stones to visit the ship and see, with her own eyes, the magnificent work he's a part of.
As a last-ditch effort, Rush proposes sitting Chloe in the neural interface of Destiny - the chair that made Franklin disappear - in hopes that it will burn away the alien parts of her, leaving the human part. Young and TJ reluctantly agree, and though she emerges safely, her condition remains the same, and her future - along with that everyone she's in contact with - remains uncertain.