Jennifer Garner's real-life pregnancy was written into the series. Her need to be on maternity leave meant that the season was cut back to 17 episodes. It also necessitated the reduction of her action scenes, hence the drafting in of Rachel Nichols as her replacement. This coincidentally gave this season a cyclical feeling with the first one, in which Sydney Bristow was guided through the treacherous waters of espionage by her handler, Michael Vaughn. In this season, Bristow is performing the same role for Rachel Gibson.
The opening scenes of this episode, including Sydney's venture through the corn-field, were clearly shot well-before the other scenes used - there are a few shots where Jennifer Garner is evidently not pregnant (for instance there's a shot of her belly when she raises the shotgun she acquires to shoot one of Vaughn's captors). However, from these scenes on, Jennifer is clearly pregnant, even though Sydney is not supposed to be (noticeably, at least) until the final scene of the episode (see in particular the party scene later on in the episode where Syd is holding a sort of hand-scarf that conveniently hides her belly from a side-view).