Combined Saga Chapter 5
Ruby, Sapphire, and Emerald were the only ones out of their group not enter Red's tower, so they were blasted off.
Ruby and Sapphire: WE'RE BLASTING OFF AGAIN!
Emerald: Okay. That saying is old. And what do you mean "again"…
The others were falling to their dooms. Red isn't shown. Perhaps he teleported or something. Anyway, Righty made a little tornado by running around, allowing the others to land safely. All Zario was doing was gazing at the burning Trainer Tower. The random people are dead, so there's no reason for any rescues. Gold's Poke Gear rings, so Gold Picks it up and it was Professor Elm wondering if the group's alright.
Dill is on the Hoenn Battle Frontier island, which was destroyed due to an earlier event (which explains why the Hoenn Frontier Brains in the anime are in Kanto). In the middle of the island, he sees a strange object.
Dill: hey, wait a minute, I remember having this thing. What the? This one has a "1" on it. Strange. I wish I could see the one I have.
Dill looks at the sky while everyone else takes the teleporter back to Indigo Plateau. Gold thinks Red could be in Mount Silver, so everyone heads there to check it out (because for no reason, people trust Gold.)