FATE [BOOK 3 of The Bond Series]

After beating the Kalos league and moving on, Greninja decides to part off with Ash, after finding out Zygard needed Greninja's help. With Greninja gone, Ash feels like he should've regretted it but let's it go. And after 2 years of departure, Greninja finds there has been Pokémon all over the region getting attacked by an unknown Pokémon. Greninja feels as if someone was trying to draw him out, and solve a mystery. And after hearing this, Ash rushes to his long time no seen friend.

When the mystery is solved they reunite after Greninja solved the puzzle, they are captured by a team of black suited figures with deep diving suits. They bring them to a deserted underwater facility, miles deep into the ocean, but someone arrives...

Someone they hadn't seen in a while.

The Prequel to Endless.
The Sequel of Lost Ninja.