Team Rocket heads back to the Team Rocket Headquarters.
Serena leaves the group and heads to the Hoenn region to participate in Pokemon Contests, arriving there sometime later.
Ash separates from Clemont and Bonnie, leaving the Kalos region and returning to Pallet Town.
The Solrock and Lunatone souvenirs that Team Rocket drops at the airport while returning to the Team Rocket HQ in Kanto are likely a reference to the Sun & Moon series.