In the chaos of the prison riot that took up all of Season 5 of Orange is the New Black, new alliances were formed, friendships were tested, and romances blossomed. That was certainly the case for Alex and Piper, who were engaged by the end of the season. But not everything went smoothly for the happy couple, and after the CERT team invaded the pool during the breakup of the riot, Piper and Alex were separated. The beginning of Season 6 sees Piper desperately trying to find out what happened to her fiancé. So where is Alex in Season 6 of Orange is the New Black, and why was the couple separated?
Piper spends the first few episodes of Season 6 completely convinced that something terrible has happened to Alex. And who could blame her for thinking that? After all, the last time she saw her, Alex was being dragged limply away by members of the CERT team in the standoff in the Litchfield pool. When Piper was loaded onto the bus along with the others who were caught in the pool, Alex wasn't among them. Piper pleaded with the bus driver to wait for Alex to appear, but the driver insisted that everyone who was supposed to be on the bus was already there, and they pulled away without Alex.
Piper is understandably desperate to know what has happened to her fiancé. But in the first few episodes of Season 6, she isn't given any answers. Alex still hasn't appeared in Litchfield Max, where everyone else found in the pool was sent, and Piper became convinced that something terrible had happened to her. Her fellow inmates grew impatient of her constant questioning, and eventually Red's new roommate, the manipulative "Badison," trips Piper, splitting her lip, chipping her tooth, and landing her in the medical unit. Piper hoped that she could find Alex there, so it was sort of a favor.
But Alex was nowhere to be found, causing Piper to become even more convinced that she had been killed by the CERT team. That fear was only confirmed when Red, in an attempt to get the message to Piper in Max that the Piscatella had been killed at the pool, sent her a code which read "the tall one dead in the pool." Red meant Piscatella (who was super tall, among other things) but Piper interpreted "the tall one" to mean Alex. Also tall.
The whole misunderstanding has a happy ending for Piper and Alex, since it turns out that Alex is very much alive, and, shortly after Piper believes to have learned that her fiancé is dead, the couple reunites after being assigned to the same cell block. It turns out that the CERT team took Alex to a medical unit, given that her arm was broken during the riot. The two have a teary, emotional reunion, only to be interrupted by a CO (this is still prison, after all).
But though Piper and Alex might have gotten a happy ending, the misunderstanding did not come without serious consequences. Piper was incredibly distraught when she was brought before the investigators seeking to punish those responsible for the Litchfield riots, telling them she didn't care about any of it anymore, now that Alex was gone. Since she was distressed and detached, when the interrogators asked her why Piscatella was in the pool to begin with, Piper inadvertently threw Red under the bus.
"I guess Red? She made us bring him down there," Piper tells the investigator when he asks her who brought Piscatella to the pool. "She wanted to torture him for torturing us. She couldn't let it go. Her f*cking obsession brought that crazy man into the prison, and now Alex is..." she can't finish her sentence as tears well up in her eyes. Piper takes a plea deal, attaching six more months onto her sentence. She's transferred to gen pop, while Red remains stuck in solitary.
Piper immediately realizes her mistake when Alex returns. Though Red initially has complete faith in "her girls," as she calls them, those girls quickly begin to pin the blame on her for Piscatella's death, rather than risk taking the fall themselves. Piper was a major contributor to Red becoming the main target of the prosecution's case against the rioters. So it's a good thing that Alex isn't dead, but her absence had a huge effect on some of the other women's livelihoods.