The Supreme Intelligence transforms into its comic form in a Captain Marvel deleted scene. Taking place in the past of the Marvel Cinematic Universe, Captain Marvel was able to tell a mostly standalone story. The film worked as an origin story for Carol Danvers (Brie Larson), but also introduced audiences to the shape-shifting Skrulls and shed more light on their longtime enemies, the Kree.
While Guardians of the Galaxy first introduced the Kree to the MCU, Captain Marvel allowed viewers to visit their homeworld of Hala. Carol spent several years on the planet training to be a member of their elite special unit, Starforce, as she learned to control her incredible powers. Beyond the hi-tech capabilities of the species, the Kree are ruled by a being known as the Supreme Intelligence. This being is a collection of the greatest Kree minds that ever lived and shows whoever is communicating with it the person they admire most. For Captain Marvel, that meant it looked like Dr. Wendy Lawson aka Mar-Vell (Annette Bening). But, its true form is a giant green head with tentacles coming out of the top.
Thanks to a newly revealed deleted scene from Captain Marvel that came in Marvel Studios' The Infinity Saga box set, the Supreme Intelligence's true form is shown. The scene plays out similarly to Carol's final confrontation with the Supreme Intelligence in the movie. The key difference in this version is when Carol blasts the Mar-Vell lookalike back, it lands in a pool of water. This is when the Supreme Intelligence's real form emerges and tells Carol, "We're not done." She promptly responds by saying, "Right... how do I put this? Yeah we are."
The idea of having Supreme Intelligence's true form featured in Captain Marvel is something that was revealed earlier this year. Now that fans can see (or read) how the scene played out, what was the reason for this version not being used? According to production designer Andy Nicholson, it came down to the focus of this scene. When the giant green head is revealed in this deleted scene, it is difficult not to just focus on that reveal. But, Marvel felt it would be best to not have this possible distraction from Carol's transformation into a fully-powered Captain Marvel.
If this deleted scene was kept, it admittedly wouldn't change much about the overall scene anyway. That said, it would establish this form for the Supreme Intelligence to use in possible Captain Marvel sequels. Considering Captain Marvel ends with Carol sending Yon-Rogg (Jude Law) back to Hala to warn the Kree that she is coming to stop them, it is plausible that future movies will show how this conflict ends. If that is the case, the Supreme Intelligence's true form could be featured without needing to explain the difference. Since Marvel ended up not using this version though, Captain Marvel 2 or any other movie that utilizes the Supreme Intelligence's final form will need to explain to audiences who they are looking at.