User blog comment:Awayorafk/Believe. The Indoctrination Theory./@comment-5218032-20140720165141

People think the eyes have so much significance. I think both the Illusive Man's and Saren's eyes are implants or prosthesises.Saren has a bunch of synthetic modifications in his body,but not necessarily Reaper tech (not before Sovereign made modifications on him). In ME2 Shepard's eyes look the same as the Illusive Man's but it has a red glow instead of blue,if he didn't remove the scars and chose the renegade path. That's probably because when Cerberus reconstructed Shepard's eyes they used synthetic implant or something like that. In the control/synthesis ending Shepard's body is being degraded into synthetic material,that explains the eyes thing.