[Matrixbeast]

Eiji wanted to help everyone.
With Shinji out of the coma and the Greeed gone, there was no real reason for him to stick around. We're shown that the talks with Hina and the rest of his friends still, so it's not like he just abandoned them.

And we've been shown what his true desire was. Remember when the one dinosaur Yummy (The one who eliminated one's desire by materializing it and destroying it). We saw that Eiji's true desire was for the world. He may have summed it up as "Power" during his fight against Ankh, but really, Eiji's desire was too great and grand. He doesn't just want to help people. He wants them to be happy as well.