Religion is always on Jean's mind – he is a Salinger wonder-kid after all. The epigraph to Nine Stories the collection that contains "Blue Period" is a Zen Kōan. Jean tells the Yoshotos that he is "a student of Buddhism" (54). There is some indication that he did so because he assumed the Yoshotos were Buddhists, and that if he'd know they were "Presbyterians" he would have said he was a student of Presbyterianism. He also claims to be an "evil-minded monk" of an unknown religion (68). Sister Irma is, of course, Catholic.
Jean is seems particularly concerned with the crucifixion of Christ, which, he thinks, is the subject of the painting by Sister Irma with which he is impressed. For Christians, Christ is the ultimate martyr. As we'll see in a moment Jean doesn't want to be a martyr. This might be why he's more interested in the Mary Magdalene figure in Sister Irma's painting. He seems to identify more with Mary, a kind of outcast accepted by Christ, than with Christ himself. He wants to be loved and accepted more than he wants to be a religious leader, or saint.
This is what he's getting at in the preface to his second epiphany:
I'm about to touch on an extraordinary experience, one that still strikes me as having been quite transcendent, and I'd like, if possible, to avoid seeming to pass it off as a case, or even a borderline case, of genuine mysticism. (To do otherwise, I feel, would be tantamount to implying or stating that the difference in spiritual sorties between St. Francis and the average, highstrung, Sunday leper-kisser is only a vertical one.) (82)
Jean doesn't want us to think of his experience as a mystical experience; that much is clear. But, let's break down the potentially confusing statement in the parenthesis. "[S]ortie" means "attack." St. Francis de Assisi devoted his life to helping lepers and other "outcasts." His mode of "attack" was to remain constant and vigilant in his work. A "Sunday leper-kisser" on the other hand, empathizes with lepers and outcasts, but isn't prepared to devote his or her life to their aid and care. The difference between the two is not just vertical, but horizontal, therefore total. The two groups, according to Jean, are worlds apart.
Jean seems to identify himself as belonging to this latter variety. He wants us to understand that his experience was a personal spiritual experience. It helped his deal with his mother's death, and helped him learn to be a kinder person. It wasn't a message from god telling him to follow a certain religion or to bring that religion to others. If anything, the message is universal and simple: don't be so hard on people, including yourself.
So, if his experience isn't wrapped up in a specific religion, and if it wasn't mystical, then why, does he write, "Everybody is a nun" in his diary after the experience? Head on over to "What's up With the Ending?" for our thoughts on the matter.