Timeframe
The events of the first season of Alias begin in 2001, the same year the series first aired. A reference to Homeland security midway through the first season suggests the series begins not long before, or not long after September 11. (The series, in fact, premiered 19 days following the 9/11 attacks.) Though there was reference to such a part of government, the federal Homeland Security department was not established until 2003. (Aside from the Homeland Security reference, there is no explicit reference to 9/11 in the first season; however, there is a reference to Osama bin Laden and a reference to the War on Terror in two episodes in season 2). In season 1, each episode covers roughly the events of one week in Sydney's life, thus each episode is said to take place a week apart, although this pattern was not maintained throughout the series. In several episodes, references were made to actual real world events. For example, in one episode, Sydney suggested to Vaughn that they should catch a L.A. Kings game, and that they'd be taking on the Islanders. This actual game took place roughly around the same time the episode was broadcast on January 20, 2002.
The season 2 finale, which sees Sydney lose two years of her life, would suggest that the series as of the start of season 3 takes place two years ahead of "real world" time, however the series was not always consistent in maintaining this. For example, in season 3 episode 17 (airdate March 28, 2004), the date March 26, 2004 was shown on Lauren's event calendar. For most of the episodes in Season 3–4, the writers avoided mentioning any current calendar dates in any episode. The one fact that did contradict this was the date on the tombstone of the supposedly dead Irina Derevko, which, when calculated, would suggest that the show was still running on "real world" time rather than 2 years in the future. However, a statement made by Sydney in the fifth season premiere "Prophet 5" regarding the length of time since she first went undercover at SD-6, is in keeping with the established timeline. And finally, the timeline seems to jump back one more time. In the season 5 episode "Out of the Box", character Renee tells Dr. Desantis, the genetic double of her father from the cryogenic box that it is currently 2006. This appears to be the first direct reference to the actual date of events. In another episode of the same season, a hockey magazine received by Sydney indicates the date to be November 2005. Also in season five, Nadia Santos' hospital admission bracelet following her recovery in the episode "30 Seconds" reads "04-23-05" and she mentions that it has almost been a year since she was hospitalized.
No time elapses between the end of season 1 and the beginning of season 2, and there are two years, one month, and several hours between seasons 2 and 3, 3 and 4, and 4 and 5 respectively (in addition, the events of the season 5 premiere episode take place over the course of 4 months). Given that there were roughly three to four months between the airing of the first few seasons, an 8-month interval between the broadcast of seasons 3 and 4, and a 4-month hiatus in the midst of season 5, by the final season Alias would only be a matter of months ahead of real-world time, making the 2006 statement plausible in the timeline. The series finale makes a further jump forward of several years (c. 2014 based upon the age of Sydney's daughter).
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