Routes

Before you leave you pick a route and go down it: it doesn't change halfway. Each one has its types, its hazard, its resource and its guardians.

What you find as you go down

Every floor
Normal floors
The route's enemies and, sometimes, a lost Pokémon or the Kecleon shop.
Every 5 floors
Alpha
A much tougher enemy. You can't keep going down until it falls.
Every 10 floors
Escape Rope
It shows up when you beat the alpha. It takes you back to the haven with everything you picked up and the Pokémon you rescued.
Floor 25
Guardian
A legendary in its room, with the Escape Rope before you go in. If you beat it, you can start your next expedition on the following floor.
From floor 26
The deep layer
The route changes: a new hazard, one more Pokémon type and its own alpha.
Floors 50, 75, 100
Guardians of the deep
A different one at each stop. After that, the route goes on with no end.