||The Enemy Walks In
||Sydney is face to face with her mother, who shoots her. She gets away but doesnt find Vaughn. Later on a mission she happens to come across Vaughn about to be cut into by Khasinau and she rescues him. Will has to fake a heroin addiction to discredit his SD-6 article. Weiss is shot by Irina on a mission. Irina turns herself in to the CIA.
||Irina is put in prison, and the CIA wants Sydney to see her. Vaughn goes instead and gets information for Sydneys mission. Sydney doesnt take her moms advice on the mission and trips the alarm. Will is sentenced to probation. Francie makes more plans for her restaurant.
||ydney has to see her mother again for information. Jack doesnt like Sydney seeing Irina at all, and then he goes to see her himself to threaten her. The CIA puts Will through hypno-therapy to find out a code that Sark was working on. Syd goes to Siberia to get a music box but is stopped by Sark and she slips through the ice.
||Jack continued to try to get Irina moved. Sydney goes on a mission to find a map that leads to "The Bible" and there she meets Sark, who tries to recruit her. Later the CIA sends Sydney and Vaughn on a mission to retreive "The Bible" but Jack rigs the building to explode, framing Irina and effectively getting her moved as well as breaking Sydneys trust of her.
||Francie opens her restaurant. Vaughn finds out about what Jack did to frame Irina. Sydney is sent on a mission where she discovers kids who are being taught to be spies. Later she remembers something and she goes through hypno-therapy to find out that Jack tested that same project on her as a kid.
||Syndey wants to save her mom from the death penalty by telling the CIA what her dad did, but he gets to them first in order to win back her trust. Sydney and Vaughn both have to be tested for a deadly disease they could have picked up in Taipei. The Senator takes Jack into custody and decides to carry out Irinas death penalty but Sydney kidnaps him and tells him a lie to get them both off. Vaughn starts to bleed from the fingernails, the first sign that he has the deadly disease.
||Irina tells Sydney where to get the antidote for Vaughns illness. While trying to get it shes caught by Sark and forced to make a deal with him to turn over Sloanes life. Sydney gets the cure but Sark spares Sloanes life to cooperate with him.
||Passage Part 1
||Sark continues his alliance with SD-6. Vaughn fires Will from his "Project Christmas" research. Irina is temporarily allowed out of jail to help Sydney and Jack on a mission to recover nuclear devices.
||Passage Part 2
||Sydney, Jack and Irina continue on their mission in India to recover the nukes. At one point it seems Irina has betrayed them but it ends up to be an act to help them. After learning about plans of air strikes, Vaughn goes to India to save them. Sloane pays the people who are holding Emily the ransom money they demanded, planning to track them. But instead he gets pictures of Emily dead and the tracker goes out.
||Sydney and Will run into Vaughn and Alice in a bar. Marshall is sent on his first mission with Sydney. The CIA wants to get to Marshall before SD-6 so he cant tell them any information, but someone else abducts him first. The episode ends as we see Marshall being tortured by the "Evil Dentist" from season 1.
||A Higher Echelon
||Kane believes that Jack has something to do with Emilys murder, so hes in danger of her finding out about his double agent status. Irina is useful again in keeping Echelon from SD-6. Sydney and Dixon go on a mission to get Marshall back, and just in time too. Meanwhile, Sydney admitted to Francie that she had a crush on Vaughn. Francie told Will, who mentioned it to Vaughn.
||Kane goes after Jack, who goes to Irina for help finding the real blackmailer. On a mission in France Sydney and Vaughn risk going to dinner and end up getting caught, although they manage to get themselves out of trouble. After Jack proves that Kane was actually the blackmailer it turns out Sloane was behind the entire thing to keep Emily alive.
||Sloane is missing and The Alliance sends in a replacement- Anothony Geiger. Sydney learns of a server 47 that holds the key to destroying The Alliance. After Syd gets the info, Jack goes in to SD-6 to verify it but is caught by Geiger, who has learned that he and Sydney are double agents. Sydney then has to tell Dixon the truth in order to have him verify the info to save her dad in time. When the codes match, the CIA raids SD-6 along with every other SD office, and they save Jack in time. Sydney and Vaughn share their first kiss in the ruin of SD-6. Will and Francie also kissed. And Francie appears to be have been killed by a double pretending to be her.
||Sydney teams up with a CIA agent named Lennox, who they discover has been doubled. While trying to figure out if they have the real Lennox or not, they discover that this doubling process has been used on someone else as well. Meanwhile, evil Francie plants cameras in Sydneys room to spy on her and Sydney and Vaughn enjoy finally being able to be with other.
||A Free Agent
||Sloane takes a scientist and his family hostage to help him figure out a Rambaldi mystery. Sydney graduates from graduate school and considers leaving the CIA, but Kendall threatens that if she leaves she cant see her mother anymore. Sydney and Vaughn go to save the family from Sloane, but the episode ends in a cliffhanger as Sloane demands that Sydney drive his getaway car.
||Sloane finishes his Rambaldi device and teams up with a man named Ahmad Kabir, using the "firebomb" on his ex-wife to seal the deal. However, Sydney and Vaughn manage to save the ex-wife just in time, but are horrified by what they see. Desperate to get this weapon back, Sydney is sent to Kandahar but is captured. Vaughn has to convince Dixon to come back to help get Sydney out, which he does.
||A Dark Turn
||Sydney learns that the CIA is investigating Vaughn for suspicious activity. Francie seems to be hypnotizing Will in his sleep to get information. Jack and Irina set up a mission for Irina to meet with Sloane, planning to capture Sloane so that Sydney will resign from the CIA. Instead, Irina uses Sloane to escape and gives him the Rambaldi manuscript they had recovered earlier.
||Truth Takes Time
||Jack is in charge of the mission to catch Irina, Sloane and Sark. They track her with a tracking device Jack planted but she gets away. Emily goes to the CIA to turn Sloane in. They bug her and wait for Sloane at his house, but Emily backs out and tells Sloane of the bug. As Irina, Sloane and Emily try to escape, Sydney and Irina end up in a shooting fight. Sydney shoots Irina in the arm and Dixon shoots Emily while aiming for Sloane. Irina and Sloane get away as Emily dies.
||Sydney wants to save Caplan, the scientist Sloane kidnapped. She finds out that his wife Elsa is Russian intelligence, which causes Jack to think shes no different than Irina. He tells Sydney not to save him but she goes anyway. Sloane gets Evil Francie to use Will to find out who shot Emily, but Marshall discovers the breach. Then Sloane gets Francie to kill Dixons wife for revenge.
||Dixon stays on the job after his wife is killed and Vaughn worries when he sees him taking pills. After Vaughn reports him to Dr. Barnett Dixon switches test results to pass a drug test. Meanwhile the CIA is trying to find out what kind of huge event is about to happen on a date found in a Rambaldi drawing. They go on a mission to recover a fake heart that Sloane had stolen out of a man- thinking that it might be a bomb. They get the heart but it wasnt a bomb after all.
||Francie tells Sark that the CIA believes Will has been compromised. Irina, informed by Sark, refuses to allow Francie to kill Will but supports his set-up. Francie hypnotizes Will and burns the mark of the second double on his retina.
||At the CIA, a depressed Sydney confers with Vaughn. Marshall begins receiving top-secret info ? Irina is uploading the double`s DNA, as she said she would. Syd then tells Will that he`s been cleared because the downloaded DNA doesn`t match his, it`s from one A.G. Doren.