The original idea for "Yesterday's Enterprise" was made by Trent Christopher Ganino on 15 April 1989, as a spec script submitted through the open submissions policy introduced by Michael Piller in that year. This original version featured the appearance of an Enterprise from the past in the Next Generation time period, and the resultant dilemma of whether to send them back. In this version, however, no alterations were made to the timeline – the central theme was simply the moral dilemma presented.

At the same time, following a conversation with Denise Crosby at a convention, Eric Stillwell developed a story that would allow Tasha Yar to return to the series after a two-year absence. In Stillwell's pitch, drawing from classic Trek episodes "The City on the Edge of Forever" and "Mirror, Mirror" – among others – a Vulcan science team would inadvertently cause the death of Surak, the founder of Vulcan philosophy, when a trip through the Guardian of Forever into Vulcan's ancient past goes wrong. As a result, the Vulcan people would never become the logical race that is known in the Trek universe. Instead, a Vulcan race more akin to the Romulan Star Empire would be engaged in war against the other powers of the galaxy, including the remnants of the Federation. As part of this alteration, Tasha Yar would be present amongst the crew of the Enterprise-D. Ultimately, Ambassador Sarek, who was on board the Enterprise to greet the returning science team, would sacrifice himself by returning to the past and taking the place of Surak, thus restoring the correct timeline.