A system for treating an eye includes a laser light source providing photoactivating light. The system includes a scanning system to receive the photoactivating light as a laser beam and to move the laser beam over a cornea treated with a cross-linking agent. The system includes a controller that provides control signal(s) to programmatically control the laser light source and the scanning system. The control signal(s) cause the laser beam to visit region(s) of the cornea more than once according to a scan pattern and expose the region(s) to the photoactivating light. The photoactivating light causes the cross-linking agent in the exposed region(s) to react with oxygen to generate cross-linking activity in the exposed region(s). The scan pattern causes a predetermined period of time to pass between visits by the laser beam to the exposed region(s), the predetermined period of time allowing oxygen in the exposed region(s) to replenish.