Those stairs are going to lead up to another room full of crates. Because apparently neither base can have enough crates of things. In fact, in one corner of the room, there seems to be two bored looking Aqua Grunts (one male and one female) who seem to be in the process of counting...what appears to be Damp Rocks.

“Ugh, this is so boring.”

“Yeah, why do we even have to count these things anyway? It's not like they're going to go missing. We don't even use them.”

Yup. Sure is a lively day at the Team Aqua base. And yup, they have absolutely no idea anything's amiss today or that some intruders just came up the stairs. Maybe they should've seen if a crate had an alarm system instead of just rocks.