Series creators Cheryl Heuton and Nicolas Falacci, who wrote the episode, first mentioned the idea for the brothers' conflict during a season two commentary.
Charlie Eppes (David Krumholtz) and Larry Fleinhardt (Peter MacNicol), FBI Special Agent William Fraley (Željko Ivanek) arrests Dr. Phil Sanjrani (Ravi Kapoor), one of Charlie's friends, on charges of sending classified information that could assist terrorists to Pakistan.
While insisting on Phil's innocence, Charlie suggests using social network analysis to find the connection between the victims and their kidnapper.
Don, Fraley, and FBI Special Agents David Sinclair (Alimi Ballard), Colby Granger (Dylan Bruno) and Megan Reeves (Diane Farr) uncover evidence that the kidnapping victims could be planning an RPG attack on a Los Angeles school.
Their father, Alan Eppes (Judd Hirsch), asserts that the brothers' individual beliefs are at the heart of their conflict.
After the arrest, Megan tells David and Colby that she is leaving the FBI and returning to Washington, DC to finish her Ph.D. and to begin a career in counseling female prisoners, something that she had earlier discussed with Larry and Don.
During the commentary for "Protest", series creators/executive producers Cheryl Heuton and Nicolas Falacci mentioned that, for early season three, they wanted to have a story that contrasted Charlie's and Don's opinions about academic freedom.
[4] To resolve one of the issues brought up in "When Worlds Collide", the loss of Charlie's security clearance, the writers and producers developed a four to five episode storyline for season five.
Carl McGowan (Keith Carradine), a tough FBI agent created by writers to be unlikable, was brought in to investigate Charlie.
Jeffrey Robinson of DVD Talk called "When Worlds Collide" "strong" and "a pretty intense storyline".