“The Cage” was used in the two-part “The Menagerie” in TOS. The 1988 version had some scenes not show in TOS, and some were in B&W because the original color prints were lost, IIRC.
You are correct; “The Cage” never actually aired in its entirety in the series. It was rejected by the studio as “too cerebral”, but it impressed them enough that they gave the unprecedented order to make a second pilot, which won them over.
Circa 1988 there was a restored version of “The Cage” (assembled from “The Menagerie” and Gene Roddenberry’s black-and-white copy of the pilot) released on tape; sometime in the 1990s a complete color copy of “The Cage” was reportedly discovered in a Paramount film vault and aired as a TV special.