The manga adaptation of Mewtwo Strikes Back! has only ever been published in the July 1998 issue of CoroCoro. It has never seen release in a collected volume anywhere in the world.
Differences between the anime and the manga
In an interview with Animerica magazine, Toshihiro Ono states that he was instructed to include Mewtwo's origin story in the manga adaptation. Since Ono only had the movie's script to work with (the original theatrical version of the movie was released approximately two months after he had begun work on the manga) and the radio drama The Birth of Mewtwo had not been created yet, Ono created his own original explanation of Mewtwo's origin.
Mewtwo and Dr. Fuji have a closer relationship than they do in the film. When Giovanni orders his men to take Fuji away due to the experiment failing to live up to Team Rocket's expectations, Mewtwo gains the darker personality it is well known for.
Mewtwo physically talks, using its mouth, instead of through telepathy.