Mewtwo Strikes Back has two cuts: the theatrical cut and the Kanzenban (complete version). The theatrical cut is exactly what it says on the tin–the version that was screened for its initial theatrical run in Japan. The Kanzenban is a later special edition with an added prologue known as The Birth of Mewtwo, and with number of re-animated cuts, a bunch of which involve the addition of CGI.
The theatrical cut was only ever released on VHS and LaserDisc. Every subsequent release has used the Kanzenban.