A woman in commando gears sneaks into a government facility and prepares to kill the officer in charge, alone in the planning room. Meanwhile, Dr. Jason Rossick monitors her from a control room along with the killer's superior, Colonel Christine Powers. When the killer hesitates, Powers asks Rossick what the matter is but he isn't sure. Powers contacts the killer, Alpha, via verbal interface and tells her to make the good. Alpha finally lowers the gun, removes her hood, and says that she can't kill her target, and then passes out.
Rossick shuts down the training exercise and tells Power that Alpha was confused because she was forced to make a moral decision. Powers reminds him that Alpha is to follow orders, not make decisions, and that they have $30 million invested in her. Rossick assures her that he can fix the problem with a little fine-tuning and dismisses the staff for the night. After they leave, Alpha wakes up and slips outside, stealing Rossick's car. As he watches her drive away, Rossick calls in an emergency alert.
The next day, Barry and Julio arrive for work and Julio tells his friend that Sabrina is throwing a charity bash for the homeless at a new club, Apocalypse Wow. Barry isn't interested in going but Julio says that he's already arranged a date for him with Tina, and tells him to show up in something a little more hip.
That night, Barry puts on a black long coat and stops by Star Labs to get Tina. She tells him that she has to cancel because an experiment went bad and she has to write up a report. As Tina goes to her table, she discovers that someone has been going through her research papers. Alpha comes out and tells Tina that she's leaving for the night, and Tina introduces her to Barry as her new lab assistant, Alpha Webster. When Tina asks what happened to her papers, Alpha says that she was trying to organize them. After Alpha leaves, Barry suggests that he take her for his date rather than go stag, but Tina warns him that Alpha is highly intelligent but not very social.
Barry has no choice but to go to the charity party alone and Julio sends him over to the bar so that he can get directions to the hot women. Meanwhile, Alpha is on the street outside and spots Costigan and another government agent following her. She ducks into the club and runs into Barry, who offers her a seat. When he comments on the odds of bumping into her twice, Alpha casually calculates the exact odds and tells him that she memorized over 600 books because she doesn't sleep. They sit down and Alpha talks about reading a book about Lincoln freeing the slaves, and tells Barry that she's decided that she doesn't want anyone locking her up. While Barry takes it all in, Fosnight collects donations and Barry realizes that he's conning the money for himself. He goes over and threatens to arrest Fosnight, who offers him a big favor in return for being let off. As Alpha watches the two men talk, Barry reluctantly agrees to let Fosnight go.
When Alpha sees people dancing, she drags Barry out onto the floor. She quickly learns, displaying expert moves, while Costigan and his partner come in and spot her. When she sees them, Alpha slips out the back while Barry is spinning out of control trying to keep up. He runs outside after her and finds more government agents surrounding his new friend. She insists that she isn't going with them and Barry stuns one agent. Alpha takes out the other three, easily tossing them away, and Barry's opponent stuns him from behind. Alpha runs away and one of the agents shoots her in the right arm. Costigan tells him to stop and the Flash recovers, tying them all up. He demands answers from Costigan, who refuses to talk. However, his wallet confirms that he's with the National Scientific Intelligence Agency. Costigan warns that he's on government business but the Flash doesn't believe him and leaves.
Barry returns to Star Labs to track down Alpha with Tina's help. They discover that someone has broken into the lab and spot a trail of blue liquid. Following it, they find Alpha hiding in Tina's lab. Alpha hesitantly comes out of hiding and reveals the "wound" in her arm: a damaged arm mechanism.
As Alpha repairs herself with parts from the lab, she explains that the NSIA built her as part of a secret project. ALPHA stands for Artificial Lifelike Prototype Humanoid Android. They wanted a programmable assassin and she is the first in the line, but they made the mistake of giving her the ability to make decisions. Rather than kill, Alpha ran away from the NSIA but they want her back. She sought out Tina because Tina had unwittingly contributed to her construction when she worked with Rossick on a program for artificial limbs for the handicapped three years ago. After Tina left the project, Rossick took her work and joined the NSIA. Tina takes some x-rays of Alpha, who asks for help altering some of the circuits inside her.
Before Alpha can explain further, Powers and her team arrive outside. They call on the intercom and inform Tina that they have a Federal warrant giving them entrance. Alpha explains that Powers is in charge of the project and is in charge of recovering her and wiping out her memory circuits. Tina remembers Powers as the reason that she left Rossick's project three years ago because of her attitude. Tina has Barry hide Alpha in the storage room and then lets Powers in. Powers has learned Alpha is there because of her job application and knows about Barry from his earlier interference. Barry comes out of the back and Costigan searches the supply room while Powers tells Tina to stay out of her away. Costigan reports that there's nothing in the storage room and Powers leaves with her people. Once they're gone, Barry confirms that Alpha slipped out through the window and starts searching the city for her.
Fosnight is going down the street when a gang stops him and demands money. They beat him up but Alpha comes by and comes to the hustler's defense. When they refuse to leave, she tosses them aside and they run off. Fosnight hears the police coming and takes Alpha to his apartment to hide her. As he tends to his injuries, Alpha finds a deck of his cards and he offers to demonstrate how to play Three-Card Monte. The android easily wins and explains that she can identify the cards because of her x-ray vision. Fosnight is skeptical until Alpha demonstrates further, and he tells her to stay put until while he runs an errand.
Barry fails to find Alpha and returns to Star Labs, and Tina shows him the earlier x-rays revealing that there is a small explosive charge planted in Alpha's memory circuits. They realize that Alpha knows about it and is trying to find a way to remove it before Powers activates the self-destruct. Fosnight calls Barry and tells him that he wants to pay off his debt by linking Barry up with Alpha. However, Powers has tapped the phone lines and gets Fosnight's address when he tells Barry. As she drives to the apartment, Powers calls in and confirms that Rossick and Omega are on their way to Central City.
Barry gets to the apartment and tells Alpha that they know about the bomb. A nervous Fosnight wonders why they're talking about explosions and Barry explains that Alpha is an android. As Alpha and Barry leave, Powers shoots Barry with a paralytic drug dart and orders Alpha to surrender. She claims that they just wants to reconfigure her circuits but Alpha insists that she's alive and the alteration will destroy her as a living being. When Powers prepares to activate the remote for the explosive, Fosnight tackles her and smashes the remote, and Alpha knocks out the agents and runs off. Fosnight escapes and Powers has Costigan take Barry into Fosnight's apartment for interrogation.
As Costigan prepares to administer a truth serum, a huge figure of a man arrives with Rossick. Powers tells Barry that Omega is the next generation of androids, stronger and faster than Alpha, and programmed without any scruples. Rossick complains, insisting that Omega isn't ready for field-testing, but Powers overrides him and tells the android to find Alpha and bring her back. As they prepare to give Barry the injection, Barry fakes a heart attack and they cut him to loose to administer CPR. As soon as he's free, Barry locks them up at super-speed and then goes to Star Labs. Tina gives him an antidote to eliminate the drug from his system and speculates that Alpha is transmitting a signal that allows Omega to find her.
Fosnight goes home and finds Alpha adjusting her optic sensor. He realizes that she's an android and says that she has to get out of town before Powers catches up to her. Alpha admits that she doesn't have any money and Fosnight gets an idea on how to raise money. He teaches Alpha how to play poker, gives her his last $100, and then takes her to the Infantino Hotel. Gambler Joey C. runs a floating poker game and Fosnight convinces him to let Alpha sit in.
Tina determines that Alpha is giving off a radioactive trace and pinpoints her location at the hotel. She also picks up a second signal closing in on the first.
Alpha wins eight hands in a row and Joey C. demands to know how she's doing it. The android explains that she has x-ray vision and the gambler realizes that Fosnight is conning him. Before his bodyguard can toss Fosnight out, Omega breaks in and smashes the bodyguard aside. He then slams Alpha repeatedly not the wall until she collapses and brushes aside Fosnight when he tries to help his new friend. The Flash arrives and easily avoids the android, but discovers that it's too hard for him to hurt with his hands. When the android smashes a hole in the wall trying to hit the speedster, the Flash uses the exposed electrical wiring to short-circuit the android, destroying it. The hero slips away just as Lt. Garfield arrives with his men and takes Alpha into custody.
The next day at the station, Garfield doesn't believe Alpha's claim that she's an android. Barry arrives and confirms her story. However, Powers and her men come in with a Federal warrant and inform Garfield that his prisoner is now theirs. When Alpha starts to put up a fight, Powers tells her that she has a new remote to trigger the explosive and takes her prisoner away.
Back at Star Labs, Barry and Tina try to come up with a plan to break Alpha out of the high-security NSIA facility. Barry warns that it has more security than even he can get past and Tina gets an idea. They pull up outside the facility in a Star Labs mobile lab and Tina hacks the security computers. She sets off false alarms and the guards keep calling Powers, who is supervising Rossick's disconnection of Alpha's decision-making circuits. She finally tells them to shut down the security and investigate the fault. Once the security systems are off-line, Barry speeds in, disconnects Alpha, and gets her out before Powers can reactivate the systems. Once he's back at the van, Barry has Tina wipe out all of the project records. Rossick realizes what she's doing but is unable to stop it. Powers, realizing that she's been beaten, sends the arming signal to Alpha's explosive implant. When Rossick warns her that the explosion will kill everyone within 50 yards, Powers ignores him.
In the van, Alpha realizes that the bomb inside of her has been armed. She warns Barry and Tina that they have 30 seconds until the second signal sets off the explosion. Tina calculates that the range of the signal is approximately ten miles and Barry grabs Alpha and runs as fast as he can away from the facility. When the second signal is sent, Alpha is out of range and safe.
The next day, Tina sets up Alpha with a new identity as a lab assistant at Star Labs East and has asked a friend to help protect the android's identity. They figure that Powers and Rossick will be too busy answering to the government for the loss of the project files to make another attempt to recover or destroy Alpha. Fosnight arrives to take Alpha to the airport for her flight to New York, but Alpha uses her x-ray vision and points out that he's changed the tickets. Barry checks and discovers that Fosnight has booked two seats to Las Vegas and decides that he and Tina had better go along make sure Alpha gets on the correct flight.