You get a wish if you meet with the Goddess at the Tower of Destiny. But before you can do that, you have to collect five gemstones.

I... only could find three of them. Mitsuru - the other Traveler - he's found four already. And he knows where his final gemstone is, too. Even if I tried catching up, there's no way I'd be able to make it in time.

[He can't look her in the eye. He knew it would turn out something like this, but... he also felt that she at least deserved to know. For when he eventually left for good...]