There we, and Xavier, see some footage of a stray air-conditioning unit being destroyed by an optic blast from a young teen. He suggests to the Feds that he be allowed to act as an agent of the government in contacting the mutants they have leads on. One of the Feds here is Fred Duncan, as seen in issue #2. It's interesting to see here the series making such tight continuity links in an era when comics were still mostly ephemera - it had been four whole years since then.
From issue #39 to #42, we focus on Scott's story. He's not the first X-Men to be given an origin story (Hank and Warren had brief treatments earlier on), but nothing this extended has been attempted so far. The action picks up as young Summers destroys the aircon, outing himself to a hostile crowd. He quickly runs away, and decides not to go back to the Sunset Orphanage, instead going freighthopping. Xavier and Duncan discover Scott has gone missing, and interview his optometrist who had filed a report to the FBI on him.
Apparently, Scott had mildly glowing eyes, and recurring headaches, for which he was prescribed coloured lenses (which is in fact a perfectly good thing to give migraine sufferers). It was either good fortune that he was wearing the ruby lenses when his powers manifested today, or perhaps an indication of something more sinister. We finish as Scott flees from some hobos who tried to rob from him.
He enters a nearby cabin, and finds another mutant, Jack Winters/Jack O'Diamonds/Living Diamond. Winters has a very confused set of powers (we see him teleporting, have diamond hands, and using telepathy), which seems to be science-accident in origin rather than a traditional mutant emergence. Anyhow, Xavier rescues Scott from him, and takes him off to be the first student in the school, where he gives him his early costume, a visor, and his mutant name: Cyclops.
Later, much later, we'll learn more about the orphanage that Scott was in, and how he came to be there, but for now it's just a cigar.