Well Evangelion 13 is a Seed of Life. Part of the system that the universe has for creating life forms. It could open the Doors of Guf and either flood the world with new life forms (Evangelions: beings of godlike power). Or call back all human souls. So I don't think your Emperor can stop a giant (covered in immensely thick armor) from performing a ritual to end all life. There is only one way to stop a being of godlike power. And that is to pierce its core with a Lance of Longinus and seal its soul. There are only two on earth. And since Eva13 (Adam) is in control of them, he is invincible. But it's special. There was only one Adam, but an experiment turned it into four and removed it's soul. So it can't be destroyed unless its core is pierced be the Lance, and then subsequently removing removing the two souls that give it life.