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As explained by Erica Simmons, Orb's engineer, SEED mode is actually an acronym.
Superior Evident Evolutionary Destined-factor
What exactly is SEED mode? Well, currently only three people have shown knowledge to this ability. Erica Simmons, Orb's engineer, had somewhat fair knowledge of this. Reverend Malchio also mentioned this to Kira in Gundam SEED. Andrew Waltfeld refered to people who possessed the seed as Beserkers. Although this is still a bit of a mystery, it seems to be a way of tapping into the person's hidden powers and abilities. SEED mode seems to be activated whenever the person is under anger and desperation. This has only been seen activated during battles, where the person is undergoing a lot of pressure. As the person becomes desperate, their determination and drive seems to increase and SEED mode is activated. When this happens, the person who possesses the "seed" undergoes a physical change in their pupil. This is one of the physical signs of a person who is in SEED mode. A mental change in the person is their enhancement in physical and mental abilities. The person's spiritual drive is boosted and their mind and body seems to coordinate better and therefore increase their overall ability in combat. The person is more focussed and determined than before, thus overcoming many difficulties in battle. This is also an subconscious process. There have been no signs of the pilot actually knowing that they are in SEED mode. There is evidence that SEED mode is not caused by enhancing genes. This is because Cagalli, who is a Natural, has SEED mode. So, SEED mode is most likely to be a hidden ability a person can tap in to.
WHO HAS SEED MODE? So far, only five characters have been seen with SEED mode - Kira, Athrun, Cagalli, Lacus, and Shinn. It was thought that only Coordinators could tap into SEED mode because of their enhanced genes. But Cagalli has been seen to also have the SEED, so therefore both Coordinators and Naturals are capable of triggering SEED mode.