>Why was he killed?

After his rift with the NOI Malcolm X became a true Muslim and, as El-Hajj Malik El-Shabazz, he returned to the U.S. and founded the U.S. branch of the Organization of Afro-American Unity. The OAAU resolved to establish a non-religious and non-sectarian program for human rights.

IMO the stage was being set for Shabazz to address the world which threated the status quo in the U.S. It was easy to label Malcolm X as a reactionary, or a demagogue within the gates of the U.S. but in his new role he was positioned to build bridges and advocate for human rights all over the globe. This would have eventually led to the toppling of the U.S. as a world power. I think Shabazz was transcending the limits of U.S. politics and this made his the biggest threat of all.