||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.
||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.
||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.