Throughout the series, the Intersect serves as the core of the story line, after Bryce Larkin sent the First Intersect to Chuck. Various organizations strive to obtain the Intersect, or human agents who may have the Intersect installed, commonly referred as a human Intersect.
The initial upload of the Intersect apparently took far longer than any subsequent update or download. The implication is that Chuck was receiving for what may well have been hours, since dawn arrived as the download completed.
The 2.0, by comparison, took only minutes to upload to Chuck, and updates even less time.