There is a strong argument to be made that A Free Agent is the episode in which the second era of Alias truly begins.
Phase One, in a direct attempt to reconceptualise the series, destroyed in one episode the entire conceptual framework of how Alias worked in order to eradicate the complexity of the double-agent spy narrative Sydney Bristow found herself within, collapsing SD-6 and the Alliance beyond them like a house of cards in swift, stylish fashion. Double Agent, succeeding it, was originally meant to air ahead of it, and serves as an unlikely breakwater, geared around a major A-list guest star and while it introduces a key part of the series’ mythology in the Helix doubling technology, it feels strangely divorced from what came before and what follows after. A Free Agent is the direct follow-up to Phase One. It is the episode that deals with the fallout and consequences of SD-6’s collapse, on multiple levels, and kickstarts the new threat Season Two will deal with.
Namely: the threat of Arvin Sloane as a super-villain, freed from the restrictions of his role in SD-6, and allowed to blossom into the character Ron Rifkin has steadily, through the nature of his ambiguous and deadly performance, steered the character toward. A Free Agent also, directly, even up to the nature of its title, deals head on with the reality of Sydney’s existence in the espionage world. She has always been a reluctant hero, dragged into the CIA’s mission to destroy the Alliance after the loss of her fiancee. All she wanted, upon learning the truth about SD-6 and Sloane, was to escape. “I did everything for the CIA I said I would, and I’m done” she claims, determinedly, planning to quit the CIA. A Free Agent does something the audience, even without realising it, needed: it provides a new mission statement for Syd, at least for the time being. A reason for her to continue being a spy and for Alias, logically, to exist.
That reason, interestingly, turns out to be the realisation that Sydney, existentially, is trapped. A Free Agent establishes Sloane as a personal and ideological opponent she needs to, logically, overcome in order to escape this life. The title becomes an ironic one.