Messenger was placed on administrative leave following an allegation that he had inappropriately touched an adult, male student. Messenger denied the charge but nonetheless decided a few weeks later to step down as pastor of the university parish.
While chaplain for over 10 years, Messenger would use the now defunct USC Catholic Community website as a platform to promote his heterodox views.
On the topic of celibacy, for instance, he wrote:
"I, for one, did not choose celibacy. I chose priesthood and accepted celibacy because there was no choice. I do not consider myself to have been free. There was simply no other way to be ordained."
"We must face the truth that celibacy in the diocesan clergy is abnormal. As in any abnormal situation, the individual must seek compensation."