The navi in Sefer Melakhim (II Melakhim 21:16) describes that aside from the sins that he encouraged the people of the kingdom of Yehuda to commit, Menashe also killed innocent people. In Bavel that was understood to mean that he killed the prophet Yeshayahu, while in Israel they explained that he built a huge idol that was so large that its weight killed a thousand people every day when they were made to carry it.
At the same time that Menashe is accused of idol worship and murder, the Gemara also attests to the fact that he was a brilliant Torah scholar. Our Mishna quotes a baraita that teaches that Menashe would teach 55 different approaches in Torat Kohanim – the midrash halakha on Sefer Vayikra – one for every year of his reign. Rashi explains that every year of his reign he would return to this midrash and develop new approaches to its content. Torat Kohanim was chosen both because it deals specifically with issues relating to the Temple and because its contents were considered by the Sages to be particularly difficult. The Maharsha explains that the fact that Menashe was learned indicates that whatever sins he committed were premeditated.
Having said all of this, Rabbi Yehuda’s opinion in the Mishna is that Menashe does have a share in the World-to-Come, since he did teshuva – he repented – as is indicated in Sefer Divrei HaYamim – (II Divrei HaYamim 33:13). Rabbi Yoḥanan argues that anyone who says that Menashe does not have a share in the World-to-Come weakens the hands of ba’alei teshuva – of penitents. He argues that during the last 33 years of Menashe’s reign he was a ba’al teshuva.