In the School for Gifted Youngsters the X-Men were tutored by Professor X and trained in the use of their powers in the Danger Room. Xavier provided Scott with visor made of ruby quartz to help him control his powers in the field. As Cyclops, Scott became deputy leader of the X-Men. While he was a skilled tactician, Scott's social skills were lacking. Scott had fallen in love with his teammate Jean Grey, but his reserved demeanor prevented him from expressing his actual feelings for her.

For a long time, Scott refused to admit, even to himself, that he had feelings for Jean, afraid he would be hurt again or that his optic blasts would hurt her - or anyone else he cared about for that matter. Scott also felt he was no match for his wealthy teammate, Warren Worthington III, a.k.a. Angel who was also romantically interested in Jean. What Scott did not know was that Jean actually had a crush on him too, but was too shy to make a move. Eventually they revealed their passion for each other and began to date.