After the events of Kirby: Planet Robobot, King Dedede started to build a machine. This machine was used to attack Kirby, but then it malfunctioned and opened a portal to another dimension. Dedede freaked out and as a result, pressed random buttons. His screen went black saying that Nightmare has taken control of the machine. The machine then used all of its power to combine the two worlds.
Kirby woke up to see a destructive landscape. The grass was burning, houses were destroyed, and I am not making an Undertale pun. Kirby noticed a Poke Ball nearby and opened it. A Level 5 Charmander came out of the Poke Ball. Kirby immediately noticed the Charmander's scar under its arm. The Charmander didn't want Kirby to touch it, but Kirby did anyways.
A young man walked torward Kirby. His name was Steven. He told Kirby how Nightmare and his forces attacked and took over Hoenn. Only Kirby could stop him. He gave Kirby a shiny Beldum to help him, and then he vanished.
Kirby eventually reached Rustburro City, where he entered the gym. He reached the end and encountered none other than Adeline! Something was unusually different, and Kirby noticed this right away. Adeline attacke Kirby immediately.
When Adeline was beaten by Kirby, a Dark Matter was seen floating away. Adeline apoligized to Kirby by giving him a Smeargle that knew Surf. Kirby was able to reach Dewford, where he saw Waddle Dee. Waddle Dee challenged Kirby to a battle.
Whern Waddle Dee lost, he realized that King Dedede was taken by Nightmare. Waddle Dee freaked out until Kirby calmed him down, explaing what happened. Waddle Dee stopped, and gave Kirby a Hawlucha that knew Cut. Kirby surfed to Slateport, where he ran into Yin Yarn. Yin Yarn was working for Nightmare, and stole a strange artifact.
Kirby eventually bought a bike to get to places faster. He reached Mauvile, who's Gym had a Bonkers inside. He challenged Kirby to yet another gym battle.
Bonkers lost and before Kirby ate him, he surrendered and gave Kirby a Paras that knew Rock Smash. Kirby headed torward the Meteor Falls, only to witness Magalor attacking the trainer there. Before Kirby can intervine, the Trainer's pokemon beat Magalor's.
The trainer noticed Kirby immediately and introduced herself as Zinnia. Zinnia gave Kirby a hidden ability Bagon. She explained how Magalor destroyed her villiage. After this, she left and tried to fight Magalor's leader, Nightmare, but lost. She woke up back at Meteor Falls, and her Whismur (Aster) was missing. She told him that an attack was going to happen at the top of Mount Chimmney, and flew him up there on her Salamance.