When looking for the story behind the inciting incident in 2006's Superman Returns, one might not suspect the answer to lie in 1984's Supergirl. Beyond continuing the continuity of Christopher Reeve's Superman, they wouldn't seem to have much in common. However, a close watch of Supergirl reveals a throwaway line that could explain when Brandon Routh's Superman began the five-year exodus that would separate his adventures from the classic Reeve films.
Superman Returns is a unique reboot because it's not a completely fresh start. Disgraced director Bryan Singer requested Richard Donner's permission to make it a sequel to 1978's Superman and 1980's Superman II. Seemingly ignoring 1983's Superman III and 1987's Superman IV: The Quest for Peace, the film picks up five years after Superman left for outer space to verify an astronomer's claim that Krypton still existed. Unbeknownst to him, he also left Lois Lane pregnant with his child after the consummation of their love in Superman II. Despite these connections, the five-year space mission was the invention of Superman Returns screenwriters and was not thought to be based on any detail in the Donner/Reeve films.
Eagle-eyed (and eared) viewers of Supergirl might say otherwise. Right as Kara Zor-El (Helen Slater) lands on Earth from her own interstellar travel, a radio broadcast announces "that Superman has indeed embarked on a peacekeeping mission in a galaxy, scientists estimate, trillions of light-years away." This line was added to explain why Reeve did not reprise his role in the sequel after dropping out of the production. A poster of his Superman in a dorm room and Marc McClure's Jimmy Olsen having a role still confirm that she co-exists with his version. Yet, that broadcast might indicate the exact moment when Superman left on his five-year search for Krypton that set the stage for Superman Returns.
A Case For Supergirl and Superman Return's Shared Continuity
The question remains: could this peace-keeping mission be that same five-year mission? First off, it should be noted that the only aliens seen or mentioned in the first four Superman films and Supergirl are all Kryptonians. Unless Superman was visiting Kara's family, which he wasn't, it is unknown what alien civilizations would attract him on such a trek light-years away. So far, the only other time Superman has been depicted going on such a lengthy mission was in Superman Returns. It is not out of the realm of possibility for the government to learn about Kal-El's selfish mission to find Krypton and spin it as a "peace-keeping mission" to make it more palatable to the public. If one can accept that answer, then it might work if not for one additional wrinkle.
Chronologically speaking, Supergirl came out one year after Superman III and thus likely takes place after that film. The makers of Superman Return always denied that their story had anything to do with that film, so that made Supergirl's timeline placement difficult. That is until the CW's Crisis on Infinite Earths had Brandon Routh reprise his role as Superman. During the crossover event, he said he had previously gone "nuts and fought himself." Many took that as a reference to the events of Superman III, where synthetic kryptonite splits Clark Kent and Superman into two people, and they must fight to recombine.
That means Superman III may have taken place before Superman Returns, and Supergirl would once more line up with Superman's departure. A closer watch of Superman III with that in mind makes Lois Lane's absence even more intriguing. Margot Kidder only appearing at the beginning and end of the film was caused by a real-life feud with the producers. In-universe, Lois' absence from the Daily Planet right before Superman left Earth might be why he didn't know about her pregnancy with their son, Jason. Such a detail would not only explain that plot hole but tie the Reeve films, the Routh film and Supergirl all together. Alas, Superman III has one piece of evidence that contradicts such an easy answer.
The Problem of Martha Kent
Superman III sees Clark Kent returning to Smallville to go to his high school reunion. While cleaning up the decorations, he and his ex-girlfriend Lana Lang (played by Smallville's Annette O'Toole) discuss how his mother, Martha Kent, had passed away before the events of the film. However, Superman Returns begins with Superman crash-landing on Earth on his mother's doorstep and staying with the alive and well Martha for several days. Since she is alive in Superman Returns, the events of Superman III could not have happened exactly as depicted in that film, and so its continuity with Superman Returns is disproved.
Between that and other inconsistencies, such as Krypton needing to be much closer than the "trillions of light-years" mentioned in Supergirl for Superman to still first arrive as a child, it does not seem likely that the two movies are referring to the same mission. The Superman Returns timeline likely splits off shortly after Superman II as originally stated. Perhaps events similar to the later films and Supergirl happened to Earth 96's Superman after the events of Returns, but there is no hard evidence to prove that.
While Supergirl and Superman Returns do not take place in the same timeline, it's hard to imagine the current state of the genre without them. Flawed as they may be, both films demonstrate how shared universes can elevate storytelling. Supergirl was the first movie to confirm two comic book superheroes co-existing on-screen, paving the way for the Avengers to assemble in the Marvel Cinematic Universe. And who could imagine Michael Keaton returning to his role of Batman without Superman Returns first resurrecting the Reeve continuity years later? This current wave of multiversal madness is made in their image. True, Routh and Slater's Kryptonians might not share a universe, but with projects such as The Flash and an animated Crisis On Infinite Earths in the works, they may still team-up yet.