Cloud Strife has SOLDIER eyes because he was exposed to a significant amount of Mako energy, similar to how actual SOLDIER members are.
Even though Cloud was never officially a member of SOLDIER, he underwent experiments involving Mako infusion and Jenova cells. These experiments drastically altered his physiology, resulting in the characteristic glowing blue, or "SOLDIER," eyes. This Mako exposure is, unfortunately, one of the only things he has in common with genuine SOLDIER operatives, highlighting the traumatic nature of the experiments he endured. The exposure to Mako energy fundamentally changed him, imbuing him with enhanced physical abilities but also contributing to his psychological issues and identity confusion.
