In episode one of Quantico, FBI agent Alex Parrish is found in the rubble ruin of Grand Central Terminal, but her story began Nine months earlier as she prepared to get on a plane to head to FBI training academy in Quantico, Virginia. Alex met the first recruit Ryan Booth an undercover FBI agent who was tasked to surveil Alex, but she was unaware of his motive. On the plane, Alex and Ryan both made up two undercover stories about their personal life and later had their first sexual encounter after which Alex told him that he was not her type. The other main recruits of the series were introduced to us, Shelby Wyatt from Georgia, Simon Asher from New York, Nimah & Raina Amin, twin sisters that are under cover as one person driving in from Ohio, Caleb Haas, Natalie Vasquez and Joseph Smith. In the present Alex is being questioned by the FBI about her classmates from Quantico. In the flashbacks, the NAT’s first assignments were to investigate each other’s past and find as much dirt as they could to be reveal in a later class. Shelby is questioned by Simon and reveals that she has a half-sister, and her parents died on 9/11, Nimah questions Simon and disclosed that he worked in Pakistan, Ryan questions Alex and reveals that as kid Alex mother shot her father in self-defense, Caleb pushes Joseph to the limit, and he kills himself. Caleb was terminated, and Simon forms a friendship with one of the twins. Alex later reveals to Liam that she is the one who shot her father. In the present, Alex is arrested, and Ryan is found a shot and unconscious in her apartment. Miranda helps Alex escape because she believes Alex did not commit the crime but is sure that she was framed.
In episode two it shows that back at Quantico Natalie is trying to compete with Alex during physical training and guess who is back golden boy aka Caleb Haas but, this time, as an Analyst. The NAT’s have two hours to find evidence in separate rooms in a partnership of three for future terrorist attacks. Alex is the only when to figure out that the planned attacks weren’t real and the first recruit in years to figure it out. Shelby and Caleb have a heart to heart. Elis questions Simon about his time in Pakistan. Miranda and Liam have a talk about him spying on Alex and ask him if he was spying on her too and told him to stop. Liam tells Ryan to keep on spying on Alex. Alex found out her father was indeed an FBI agent and one of the best. In the present Alex is on the news and described as armed and dangerous. Alex is on the run and the only one to back up her story is Ryan Booth, who is in surgery. Ryan and Alex later spoke over the phone where he told her that he knows that she didn’t shoot him, but the only way to buy Alex some time is for him to say Alex did shoot him. Natalie and Alex got into a fight after Alex returned to her apartment to find evidence that she was framed and discover that there is an apartment right next to Alex’s that had contents to make a bomb. Miranda is arrested after helping Alex to escape FBI custody and reveals that Liam may have fallen in love with Alex.
At the beginning of episode three, Alex’s mother house is being rummaged by the FBI, Back at Quantico the NAT’s are doing a water training exercise in which they have to work together to get free. Liam gives Alex a file about her dad and for the assignment this week, the NAT’s have to conduct profiles base on the strengths and weakness that they find in each other. The NAT’s are working on each other’s profiles, and they don’t like what they see, and Miranda tells the NAT’s that they all to submit three people that they think should be cut, or she will cut ten. Everyone at Quantico is turning against each other, and Ryan and Simon get in a fight. Simon went nto Miranda and voted and returned to the dorm and suggested that everyone does the same and Alex begs them not to turn on each other. Some of the NAT’s are about to go vote but then Miranda stops them and tells them that it was an exercise and that they are a team, and they shouldn’t turn on each other and that they were the first class ever to consider it, Simon gets probation. Simon, Ryan, Shelby, and Alex makes up. Miranda, Liam, Shelby, Caleb, Alex, and Ryan have a talk. Alex divulges that she is the one who shot her father expressing her guilt, and Miranda son is up for parole. It is also revealed that Natalie has a daughter.
In the present, Ryan is back at work after his surgery, and Liam is working hard to find Alex. The FBI brought in Alex’s mother Sita in for questioning. Alex is still on the run and seeks help from Simon, who later revealed that whoever is framing her started to do so the day she walked into Quantico. Simon calls the police on Alex but then helps her escape. Liam is convincing Sita that Alex was the one who set off the bomb in Grand Central. Miranda and Sita have a talk about not believing anything they say about Alex and not to give up on her daughter so easily. Alex’s mom talks to the press and begs her to turn herself in, breaking Alex’s heart. It is reveal that Simon is an undercover agent working with Clayton.
The fourth episode starts out with the NAT’s training, and Ryan gets to go home, but first he needs to convince Alex to leave Quantico. The assignment this week is that they are going to be put in high-stress situations to see if they can overcome their wiring and make the right plit-second decision. Miranda convinces the Nimah to come back to Quantico, and Alex struggles with what she learned about her father and fails during a training raid of a hostage situation similar to what happen to her as a child. Elis continues to question Simon, and Nimah and Raina had a heart to heart. Miranda and Ryan convince Alex to stay. Alex and Shelby admit their secrets to each other. Ryan and Alex have a talk, and Miranda offers the NAT’s some good advice. Alex finally tells her mother she is at Quantico. Ryan confronts Liam about Alex. In the present, Simon Makes a split second decision and decides to help her escape and instead of turning her in. Simon takes Alex to see a guy that knows about bombs, and they found out the wire came from Shelby’s Company. Simon and Alex sneak into Shelby’s apartment, but Shelby returns early. Shelby and Alex get into a fight, and Alex wins. Alex takes Shelby, as a hostage and the FBI give the order to no longer take Alex as a prisoner but shoot to kill.
At the beginning of episode five, Alex is all over the news and Shelby, and Alex has a talk at Shelby’s apartment. The NAT’s are really training hard, and Caleb thinks Shelby told on him about him doing gun training. This week’s assignment is that they have to go undercover and see if they can convince the world they are who they say they are. The NAT’s are going undercover at the Capitol Lane Hotel, but there is a catch they have to switch the identity’s that they made up and practice. Caleb keeps trying to blow Shelby’s cover, and Miranda confronts Liam about his investigation on Alex. Elis goes and talks to Max, Simon presume boyfriend to continue with his obsession about Simon’s past. Elis finds out that Max is not really Simon’s boyfriend, and Shelby and Caleb finally get together after a heated fight “bum Chicca wow-wow.” Alex, Ryan, Nimah, and Raina passed the test and found the person they were looking to have a meeting. The twins figure out how to work together without anyone noticing, Elis confronts Simon about the information he gathered from Max. Alex and Ryan get steamy after a few drinks and them working so closely together. Simon convinces Elis not to go Miranda with the secret about his past, and Raina and Simon's relationship grow closer.
In the present, Alex finds out she is sentenced to death, so after a snarky comment by Shelby, Alex seeks help from a group on the Dark Web to tell her side of the story. Alex meets with the members of the Dark Web group, but before they broadcast her side of the story, she has to convince them that she is innocent. Alex is able to convince them that she is innocent, and they broadcast her side, but the building she is in is surrounded by the FBI, but Alex mange’s to escape the FBI after she had a well thought out plan in place. The members of the Dark Web groups gave Alex passports, ID’s, and hotel reservation. Alex got the attention of the American people who is now questioning whether or not she is the Grand Central bomber. Shelby chooses Alex’s side after hearing her side of the story. The episode ended with a cliffhanger that instigated that Caleb could be a potential suspect in the Grand Central bombing.
In the sixth episode, Alex and Shelby watch the news and have a conversation about Caleb. Eight months earlier Raina and Simon are growing closer and so are Shelby and Caleb although Shelby seems a little skeptical. Miranda’s son Charlie is home, and she misses work to stay home and keep an eye on him. This week’s assignment is the NAT’s have to surveillance Miranda and her troubled son. The NAT’s set up surveillance in Miranda’s home. Liam and Charlie have a talk, and Caleb gets jealous after he thinks Shelby is seeing someone else. Ryan and Alex's relationship grow closer but came to a quick end when Liam accidentally blows Ryan’s cover. Charlie sneaks out, Simon tells Raina that he likes her, she shows him her hair, and they kiss. Caleb and Shelby admit their feelings for each other. Miranda and her son have an argument. Alex confronts Ryan about being undercover and spying on her, and Caleb confronts Shelby. Alex forgives Liam. Simon catches the twins together in their room, and Natalie tells Ryan how she feel about him. In the present, Caleb takes over the investigation, and Simon bugs his computer, but it turns out that Shelby's the one who Caleb is investigating. Simon and Alex find surveillance footage showing the twins at Grand Central before the attack. Caleb is the only one who has access to the surveillance footage, which Alex needs to prove her innocence. It is revealed that Shelby was having an affair with Caleb’s father, and now the twin is suspected for the bombing.
The seventh episode starts out with Alex trying to convince Simon to find the twins. At Quantico, the NAT’s face their greatest test to date where they are locked in a classroom with a bomb. The NAT’s work together to unlock the door, but are unable to defuse the bomb in time. However, they find out that the bomb is a fake. Trainees who stayed back with the team have passed the test and demonstrated their readiness to sacrifice themselves for the country and those who ran out were sent home. The Golden boy Caleb is bumped back up to NAT, and the twins are officially introduced to the class. Elis and Simon share a kiss before Elis goes home, Ryan and Alex have a heart to heart. Shelby tells Caleb’s father off. Alex blackmails Liam into giving Ryan his job back. In the present, Simon and Alex confront Raina and find out that it was Nimah at Grand Central. Liam tells Natalie to follow Ryan, and Natalie puts a tracker on Ryan. The FBI caught up to Shelby, Ryan, Simon, and Alex. They arrested Shelby, Simon, and one of the twin putting the twins and their operation in danger. Alex and Ryan escape but Ryan got shot, and Natalie caught up with them and let Alex and Ryan go instead of taking them in.
The eight-episode starts with the FBI scrambling trying to find Alex, and Ryan and Alex find shelter has Alex have to remove the bullet. Back at Quantico Nimah moved out and is now sharing a room with Alex, Raina and Simon get to know each other. Miranda brings her son to work, and the NAT’s have a bit more freedom. The assignment this week are that the NAT’s are going to be working on a test case. Ryan gives Alex new information about her dad which is that he and Liam worked together until 1993. Caleb questions Shelby honesty because of her secret phone calls, and Alex and Ryan are looking for a file on her dad. They solved the case, but now they have to reenact the crime and find the person carrying the chemical. While on the mission Shelby notice Caleb was acting off and confronted him about it and he told her everything was ok but was soon brought in by the FBI for questioning. Miranda showed up and defended Shelby telling them that she knows about Shelby sister. Shelby found out that Caleb was the one who provide the information to the FBI agents. The file on Sita went missing; Liam and Alex have a serious talk and Alex finds out the truth about her father. Caleb tells Shelby that he was in a cult, and he trusted them, and they deceived him, so he has trust issues, and Shelby forgives him. Simon makes a move on Nimah, but got rejected and went to see Raina “Raina will not be your leftover, Simon.” Miranda is found bleeding out by Alex, and she told Alex that it was Charlie that did this to her.
In the present Alex tried to cater to Ryan bullet wound, Clayton talks to the press and the members of the Dark Web hacked into the FBI system. Clayton asks Caleb to get rid of any evidence that Shelby and he were every together. The member of the Dark Web group and Alex found out that there could be another bomb out there. Caleb finds evidence that Alex is not the bomber but Clayton made every excuse for why he does not believe him. A normal person would have moved faster than The Flash to get on that plane but Alex being Alex wants to stay and help find the other bomb and turns herself in to tell them about the other bomb. Caleb confronted his father about deleting the email that proves that Alex ID used by someone else.
At the beginning of episode nine, Alex is being Mirandize. Back at Quantico after Ryan told Alex that Liam has been missing from work and that they were planning to replace him, she visited his house to find a drunken Liam and tried to help him sober up a little even though he resisted at first. This week’s assignment is in teams and is about what victim’s serial killers didn’t kill. Raina is feeling a little left out because it seems like everyone likes Niamh more than her. The NAT’s are working hard to find which victim the serial killer did not kill. Ryan gets mad at Alex for helping Liam. Miranda is recovering well, and Natalie tells Shelby about her daughter. Caleb’s father told him that Shelby sister may not exist. Alex and Ryan got into another fight because she got a phone call from Liam and she ran to his rescue but this time, he might be leaving, the NAT’s are mad at Simon after he couldn’t let go off a discrepancy that he found in the case about one of the victims being falsely accuse and he report it to the FBI but by doing so he got a serial killer back on the streets. In the present Elis is back and as a lawyer this time, and he claims that he is trying to help Alex. Caleb is team Alex finally. The agents that were sent to integrate Alex decide that if she won’t tell them what they wanted to hear they would hurt the people she loves most and torture Ryan to get her to talk, but as she was about to fabricate a story they were interrupted by Liam and another group of FBI agents. New Intel about Alex was found on the day of the bombing showing that someone grabbed her and pulled her into a van, and Natalie was finally convinced that Alex was innocent and joined team Alex. Liam finally believes Alex, but he thinks that if they set her free, they will not find the second bomb. The cliffhanger left us thinking that Simon might be behind the bombs after he is seen meeting with a friend of his, who gives him blueprints for all New York train stations. Alex pleads guilty.
The tenth episode starts out with Alex and the other agent’s agreeing to help find the bomber and the other bomb. Back at Quantico, the NAT’s are doing hand to hand combat, and Alex notices the scar on Natalie's neck is fake. Clayton keeps pushing that Shelby sister is not real, but Caleb makes a deal if he finds proof Clayton will leave Shelby alone. All the NAT’s are still mad at Simon, and the assignment this week is that they have to pair up and check the background on the future NAT’s. Caleb sneaks into Shelby’s room and does some digging. Natalie admits that the scar is fake, and Nimah is trying to get Simon kicked out. Nimah told the whole class that Simon was a war criminal, and Simon’s secret is out. Ryan finally tells everybody that he is a special agent and sticks up for Simon. Ryan and Alex admit their feelings for each other, and Simon is kicked out of Quantico for attacking Ryan on their third week at Quantico. Shelby sister turned out to be a fake using her for money. In the present, Liam and Miranda told Alex that she needs to spy on her team which she disagree with first, but was convince by Liam and Miranda that it is the best thing to do. Nimah confronts Raina about going to the hospital and kissing the guy because she is in love with him, and everyone is mad at Alex for spying on them. Simon admitted that he was the one who planned Grand Central, but someone stole the plans and used them because he said he never wanted his bombs to go off. Everyone that Alex trust is mad at her for spying on them, Nimah is mad at Raina, and Caleb is mad at Shelby. Alex goes and asks Simon for help, but he turns her down, and Simon is drugged and taken from his doorstep.
The mid-season finale starts with Alex arguing with Liam and Miranda. Back at Quantico, this week’s assignment is homework for the three weekend the NAT’s are on holiday break. The homework was to see if they can solve a still active case. Nimah, Shelby, Natalie, and Alex all lied about going home and realize that they all were staying in the dorms at Quantico. The ladies decided to drink have fun while they try to solve the case. Alex decides to call Ryan while she is drunk and he picked up, but she heard a female voice in his background and quickly hung up the phone. Nimah goes to find some wine but instead ends up in a conversation with Miranda, and Caleb convinces Shelby to come to his house for a party, and she agreed to go only if her friends could come along. Shelby was star struck when she met Caleb’s mother. At the New Year Eve ball, Alex and Ryan get into a heated conversation that leads to them making out, but she broke it up telling him that she couldn’t do it. Shelby and Caleb’s mother have a talk about Caleb. Alex and Ryan’s ex-wife have a talk about Ryan. Shelby broke up with Caleb, and Miranda returns home to find Charlie passed out bleeding.
In the present, Elis got attacked, or so he says. Alex, Nimah, and Natalie searched Simon house and found blueprints of a bomb, which lead them to a hotel room that Simon was tied up with a remote detonator for a bomb strapped to his hand. Alex was the first to realize that Simon was not lying, and then Nimah and Natalie realized that Elis was the one that framed Simon after Simon threaten to let go of the trigger. Elias comes clean about being blackmailed into framing Alex for the first bombing but admits he targeted Simon for the second because he was scared. Elis committed suicide, they defused the bomb, and Simon let go of the trigger, but it blew up the command center. Caleb is now a suspect and the command center blowing up. So the question is who was in there, who is still alive, and who is behind the bombing?