The Omaha project is a top-secret military operation that may or may not have future relevance in the Chuck plotline. Omaha was first mentioned in "Chuck Versus the Alma Mater" where Professor Flemming explains to Bryce that the CIA needs Chuck for the Omaha project: Another possible reference is made in "Chuck Versus the Nemesis" where Bryce tells Sarah "We will always have Omaha" (a Casablanca reference, originally "We will always have Paris"). Whether Omaha was intended to have any relevance in season 2 or whether the possible plot-line was killed off due to the writers' strike is unknown.