EPISODE 13 – Phase One
In this episode, the entire world of ALIAS is turned upside down, beginning with the mysterious disappearance of Sloane that brings a new head of SD-6 in Jack and Sydney's life. As the Bristows struggle to stay one step ahead of having their secret blown wide open by this new player – and Will and Francie make a startling discovery of their own – Sydney uncovers a crucial weakness, one that could bring down the entire Alliance. But to put her plan into action, first she must tell Dixon the truth…about everything.

EPISODE 14 – Double Agent
When a young CIA agent dies, suspicion immediately falls on her partner and lover, agent Jim Lennox. But after Sydney rescues Lennox from captivity she strikes up an instant connection as they discover shared wounds – realizing they've both lost someone they love to the job. Yet even her judgment is thrown when Vaughn and Jack discover that Lennox was pursuing a technology that allows people to change their appearance. Now Sydney must ask herself: is this the real Jim Lennox – or his double?

EPISODE 15 – A Free Agent
Sydney finally has the opportunity to leave the CIA for good, but a startling phone call from Sloane, combined with the kidnapping of a brilliant mathematician, brings her back into the fray.

EPISODE 16 – Firebomb
When Sloane gets his hands on a terrifying weapon, Sydney must turn to a betrayed and hurt Dixon for help. But when her ex-partner refuses any assistance, she has no choice but to carry out the mission herself.