Breed her, of course

Malamar looked left and right, making sure no other Trainers were around. He wanted to breed his new Seel.

"Seel. Seel. Seel. Seel," Misty said even as Malamar opened up his flaps and exposed his cock. Upon seeing his cock, Misty used her hands to drag herself closer to him.

"Seel seel. Seel. Seel."

Malamar grabbed her with his tentacles and gently placed her on his cock, beginning to pump.

"Seel. Seel. Seel," Misty said, her claps synching with each thrust of Malamar's cock.

Malamar, to ensure her programming stuck, used his psychic abilities to infuse his cum with hypnotic powers. Essentially, once he came, Misty would be locked into her Seel mindset. He'd still be able to program her otherwise, of course. It's just that Misty the Cerulean Gym Leader was now replaced by Misty, Malamar's horny Seel in her mind.