Picking up from #5, where Xavier decided the X-Men were ready now, the team officially graduate at the start of X-Men #7, both as X-Men, and from prep school. Xavier then leaves them under the temporary leadership of Scott. Leader-Scott immediately starts doing the things we know and love Leader-Scott for - i.e. stays in at the mansion watching for trouble while his team-mates make their first on-panel visit to a Bohemian coffee shop in Greenwich Village. Here they feel comfortable displaying their mutant traits, with Hank showing off his oversize feet, and Bobby joking about their friend who is a "super-powered mutant". It's not quite the Stonewall Inn, and Greenwich Village has been that sort of place for decades by the sixties, but makes for a curious conjunction, especially with a trans reading in mind; only amplified by Magneto's finding he can "pass" at the carnival in costume.
Back at the mansion, Scott's vigil is broken by an alert, as Magneto removes Blob's memory block. They rush to the scene and we have the inevitable nil-nil draw between the X-Men and the Brotherhood. Blob walks away, and without Xavier around to mind-wipe him again, he's left with a memory of what happened. Why has Xavier left, anyway? Well, we're not told until issue #9, but Scott does say that he was thinking of leaving the team to seek out a cure until the temporary leadership thing comes up. Xavier, being manipulative? Never. In Astonishing X-Men #14, Emma, under the influence of Cassandra Nova, says he picked Scott to lead because he had nothing else. Perhaps that's not the whole of it.