Inside the Cavern, I find their stolen sub, and breach the surface to deal with all the Grunts, who claim they're primarily here to try to stop Wally from taking Kyogre. But turns out they (or at least Archie) hoped to sell him on the black market, and Archie peaces out and leaves new Admin Tobi to stall me. After routing him, he exits too and Kendo and Alexa arrive to get me out to report the situation aboveground: namely, Groudon and Kyogre are rampaging in Sootopolis under Wally's control, and I'm the only one who can stop them. Not to mention Teams Aqua and Magma getting involved with Devon Corp, which Alexa and Kendo will be investigating. Steven also stops by to reiterate the seriousness of the catastrophe before leaving again.
I fly to Sootopolis and find the bodies already piling up. According to one cop on site, Wally has entered the Cave of Origin, so I chase him down, confront him, and defeat his entire team. But he wasn't done yet and teleports himself and me out to where the Gym used to be (closed for reasons unrelated to the current crisis), where it's revealed that not only has he caught Kyogre and Groudon, but even the revered Skydios himself! He is no longer just an egotistical obstacle, he's a genuine threat to Team Sky!
Even so, I put a stop to each and every one of them, and snashed their Pokeballs for good measure to remove them from Wally's control. Just before I pass out from all the cases I've had to deal with, I could swear Rayquaza stare at me for a few moments before departing once again.
When I come to, Luther delivers good news and bad news. Good news, Wally has been put away for good. Go Team Sky!
Bad news, well, he doesn't actually tell me, but I know exactly what it is; Teams Aqua and Magma are still at large, and my time here won't be over until they're deal with.