Cunningly presaged by the cliffhanger at the end of season one, the first episode of Alias second season confirmed what heroine Sydney A. Bristow (Jennifer Garner) -- college student by day, counterespionage agent the rest of the time -- had feared most: that The Man, the evil leader of a vast criminal cartel, was no man at all, but instead Sydneys supposedly dead mother, former KGB agent Irina Derevko (played by new series regular Lena Olin). Though Irina would eventually claim to have reformed and insisted that she was looking out for Sydneys best interests, her actions -- which included innumerable double-crosses, sellouts, and betrayals -- would seem to indicate otherwise. Even so, nothing that was ever indicated on Alias was ever quite what it appeared on the surface. Meanwhile, both of the spy organizations for which Sydney worked, the CIA and the more sinister SD-6, were dedicated to destroying the cartel formerly run by Irina and now in the hands of her mercurial lieutenant, Sark (played by another new series regular, David Anders). The two rival agencies also continued their search for the missing Rambaldi fragments, which when assembled would become a terrifying weapon of mass destruction, as well as The Bible, the operations manual used by Irinas old criminal empire.
Still embittered by the knowledge that she had been used all her life by SD-6, Syd persisted in covertly working against the organization by throwing in with the CIA, under the supervision of agent Michael C. Vaughn (Michael Vartan), who by the time season two rolled around, was making no secret of his love for Syd. Two other SD-6 operatives, computer genius Marshall Flinkman (Kevin Weisman) and agent Marcus Dixon (Carl Lumbly), likewise crossed over to the CIA, with tragic results for at least one of them. Syd was given even more reason to despise the espionage business when she learned that, as a child, she had been a guinea pig for a program designed to indoctrinate spies at an early age -- a program developed by her own father, Jack Bristow (Victor Garber). There was another father figure in Syds life in the form of her SD-6 boss, Arvin Sloane (Ron Rifkin), who despite his cruel cunning and ruthlessness was genuinely fond of both Bristows. Sloane would launch a second career as a solo villain when, disillusioned by the SD-6, he bolted the organization and set about to harness the awesome power of the Rambaldi device for his own purposes. His replacement at SD-6 was the no-nonsense Geiger (Rutger Hauer), who, shall we say, harbored no great love for either Syd or Jack. In addition to Rutger Hauer, season two of Alias would feature guest-star turns by Faye Dunaway as the duplicitous head of SD-6 counterintelligence; Richard Lewis as a CIA counterintelligence analyst investigating Vaughn; and Christian Slater as a scientist who was kidnapped by the renegade Sloane -- and whose past life experiences bore striking resemblances to those of the Bristow family.
Elsewhere, it was business as usual for crusading journalist Will Tippin (Bradley Cooper), who doggedly continued his crusade to expose and destroy SD-6 and all the other agencies in the Alliance of Twelve. The basic through line of Alias took off on a radical and wholly unanticipated new direction with its January 26, 2003, episode Phase One. In this truly shocking entry, Syds roommate, Francie (Merrin Dungey), was murdered and replaced by an exact double, thereby further blurring the series distinction between its heroes and its villains. Also in that episode, the CIA put an end to SD-6, thus freeing Sydney from her double-agent balancing act and allowing her and Vaughn to finally express their feelings for each other. But even those developments paled in comparison with Alias second-season cliffhanger finale, in which after being rendered unconscious in a fight with the bad Francie, Syd awoke to discover that two whole years had passed -- and her erstwhile lover Michael Vaughn was now beyond her reach! ~ Hal Erickson, All Movie Guide