Alias - Season 2 Synopsis

Sydney discovers that her mother is alive, holding her prisoner in Taipei, and is actually the ring-leader of an international secret espionage network. Syd is shot in the shoulder by said Mom (aka Irina Derevko aka Laura Bristow) but manages to escape.

Will's story was published and he is now in deep doo-dah, and is a target for SD-6 assassination, until Jack quickly thinks up a way to discredit Will in the public eye and save the man's life.

He injects Will with heroin, and Will claims to be a heroin addict who made up the entire SD-6 story

Meanwhile, Sydney travels to one of Mom's hideaways in France and discovers Vaughn there, semi-conscious and about to undergo unscheduled surgery. She rescues him and they escape.

Sydney returns to learn that Mom aka Irina has turned herself in to the CIA, claiming she wants to cooperate. But Irina will only talk to Sydney.

Sydney finds it rough going at first, facing her traitorous Mom, but seems to be building some relationship as she goes to Mom for info about her missions.

Sloane is inaugurated into the Alliance of 12, currently 11 . At the same time, he begins to be troubled by phone calls and flowers that seem to come from his dead wife Emily. He asks Jack Bristow to investigate quietly.

Vaughn is not happy dealing with Irina, the woman who killed his father, but he does so for Sydney's sake.

Jack is convinced that his ex-wife is dangerous and should not be trusted.

The CIA begins a venture to try to retrieve Rambaldi artifacts that Irina's organization knew about, as well as the organization's secret archives, trying to stay one step ahead of SD-6. So far they've got a music box with a cold fusion type formula encoded in the music.

Will is enlisted to help out the CIA since he now knows everything and might even remember more under hypnosis.

Francie, meanwhile, is totally in the dark about all the spy stuff and is opening a restaurant.

Jack frames Irina to get her away from Sydney. Syd finds out and Jack confesses to the CIA, getting him into deep doo dah. He gets in even deeper doo dah with Syd when she finds out he had her put in a children's spy training program when she was six. So Syd is finding it difficult to trust either parent.

Vaughn starts to investigate possible KGB connections between the spy kids program and IQ testing in the US. He hires Will to help, and Will discovers something weird happened with the 1982 IQ tests.

Francie opens her restaurant at last

Last season's cliffhanger comes back to haunt Vaughn as it turns out it gave him a deadly virus.

With help from Irina, Sydney retrieves an antidote for Vaughn's virus, but also discovers Vaughn has a girlfriend who is waiting for him at the hospital.

Sark and Sloane strike a deal to combine forces in their Rambaldi hunt, so now Sark is working for SD-6.

The Bristows strike a deal and go on a mission together to Kashmir, looking for stolen nukes and discover instead a Rambaldi device that might hold the secret to eternal life.

Sloane gets a phone call demanding ransom for the return of his wife Emily, whom the kidnappers say is alive. This time he asks the Alliance for help to find the kidnappers.

When word comes that Sloane is getting a secret portal into the the electronic Big Brother Echelon system, Irina saves the day by finding the portal.

The Alliance sends Ariana Kane to SD-6 to investigate Emily's kidnapping and death and Kane decides to go after Jack. After some investigation, Kane decides to put a tail on Sydney too, whom she is also beginning to suspect .

After a successful mission in Nice, Vaughn asks Sydney out to dinner, thinking they are far enough away from SD-6 for them to be safe, but they're almost caught by Kane's goons.

Jack is caught by Kane, but but ends up being saved by Sloane, who uses some info Jack found on Ariana Kane to have Kane arrested instead.

Sloane reveals to Jack that ever since he joined the Alliance, his conversations, locations, and vitals have been constantly monitored through an implant in his neck. Now he's got a bug zapper to trick the implant.

With no monitors, Sloane secretly heads for the Philippines, where Emily is alive. Seems Slaone and Emily faked her death, bilked the Alliance out of ransom money, and freed Sloane of his monitor.

Will and Francie celebrate his new job at a travel magazine (actually a CIA front) and her restaurant's success with a lobster and a make-out session.

With Sloane away, SD-6 gets a new chief named Geiger, who goes after Sydney and Jack.

Syd hears about a secret server that controls all things Alliance. Suddenly, they have the means and so the CIA raids SD-6 and coordinates raids on all Alliance headquarters, thus bringing down both SD-6 and the Alliance at once. No Alliance and no SD-6 means that Sydney and Vaughn can at last kiss

After the raids, Sark calls Sloane and reveals that Sloane orchestrated the intelligence leak to Sydney that led to the secret Alliance computer. He also reveals that a genetically altered operative of Sloane's has killed Francie and taken her place.

Sydney, graduating from grad school and hoping to put her spy days behind her, gets a call from Sloane, who confesses that he engineered the whole Alliance downfall. Now she'd rather stay in the biz and get her ex-boss.

After the fall of SD-6, Marshall goes to work for the CIA as their newest tech wizard. But Dixon, disillusioned and with a wife who does not want him to be a spy, decides to leave the biz.

But when Syd is kidnapped, Dixon comes back to save her and joins the CIA.

Jack persuades the CIA to let Irina and him go after a Rambaldi manuscript. Only problem is that Irina escapes CIA custody and joins Sloane with the manuscript.

Emily joins Sloane in Europe, discovers that Syd's mom is not dead and that Arvin is still a bad spy. So Emily decides to turn in Arvin to the CIA but gets caught in the crossfire and is killed.

Using hypnosis on Will, NotFrancie accesses satellite footage, so Sloane knows that Dixon killed Emily. Tit for tat, Sloane has Dixon's wife killed.

Sloane, disillusioned since Emily's death, goes to Tibet to visit a monk who was the one to introduce him to Rambaldi. What the monk shows him this time sends Sloane to complete Rambaldi's plans.

The CIA trace the satellite intel leak to Will's account, and they arrest him but he escapes.

Irina confesses to Sydney that she turned herself in to the CIA in order to find out where the US cache of Rambaldi stuff was, that she struck a deal with Sloane to add this stuff to his cache, and that she loves Syd and Jack and will help them. She disappears before Syd can say I don't believe you.

Irina sends the intel to clear Will, who tries to find out who framed him.

While Syd and Co are in Zurich checking out a warehouse, where Irina says Sloane stashed his Rambaldi stuff, Jack and another Rambaldi artifact are captured by Sloane. Sloane tells Jack he now has the makings of a Rambaldi machine called The Telling. The warehouse raid was fruitless, and Irina realizes that Sloane must have known she would betray him.

Again following an Irina tip, Syd and Co raid a building in Mexico City, where they find Jack and almost capture Sloane. Irina who is also there escapes after telling Syd she is the prophesy gal and that she must stop Sloane.

Will discovers that NotFrancie is a double, and a bad guy, and is stabbed by same. When Syd gets Will's message, the gals have a fight to the death, with Syd finally shooting Francie and then passing out herself.

After passing out, Syd comes to in an unfamiliar alley in Hong Kong. She calls the CIA and waits at a safe house until Vaughn arrives. He has some very disturbing news. Although Will is still alive, Syd has been missing for two years and she was presumed dead. Syd has some disturbing observations, like a scar on her stomach that was not there before and like the wedding ring on Vaughn's finger.
And so goes Season Two.