The secret ritual that Jesus used to initiate his followers, argues Morton Smith, may have been “limited to a few, shut away from the rest by special requirements, and at last quietly forgotten.” Both Morton Smith and Scott Brown argue that Clement of Alexandria may have taken Secret Mark with him when he fled Alexandria during the Severus persecution of 200 CE. Origen who was a teenager at the time of the persecution and who may have been Clement’s pupil, says nothing of Secret Mark and had a very different notion of the secret tradition than did Clement. For Origen, the secret teachings were found hidden in the scriptures—one just had to know how to find them—rather then being a secret initiation. Since Origen was a teenager when Clement left, he likely would have been too young to be initiated before Clement left, and if Clement took the letter with him, perhaps the higher initiation was no longer performed in Alexandria after Clement left.
Furthermore, in the second century, sectarian groups that moderns label Gnostics, claimed to have access to higher secret oral teachings from Jesus. As a result, there was “a devaluation of oral traditions,” says Guy Stomousa. “This devaluation was apparently the result of a conscious effort to prevent the exploitation of secret traditions, which could hardly be controlled by the hierarchy.” “Since Christian intellectuals, such as Irenaeus,” argues Stromousa, “were fighting Gnosticism with all available weapons, this predilection entailed the imperious necessity for them to deny the existence of esoteric traditions within ‘orthodox’ Christianity.” Bernard McGinn argues, “The most important effect that Gnosticism had on the subsequent history of Christian mysticism was to make esotericism of any sort suspect.”
Nevertheless, notions of a secret initiation persisted. Stromousa cites Gregory of Nyssa (c. 335–395) saying that like Moses “the public appoints someone able to become initiated in the divine secret, and then trusts him when he reports to them. Gregory adds, however, that ‘nowadays, this is not observed anymore in many churches.’” Furthermore, many of the fathers claimed that many aspects of the baptismal and Eucharist liturgies derived from a secret tradition. In Basil the Great’s (329-379) De Spiritu Sancto, he cites a number of practices that the church performed that are not found in the scriptures, such as the sign of the cross, praying facing East, consecrating baptismal water, and baptizing three times.
And as to the other customs of baptism from what Scripture do we derive the renunciation of Satan and his angels? Does not this come from that unpublished and secret teaching which our fathers guarded in a silence out of the reach of curious meddling and inquisitive investigation? Well had they learned the lesson that the awful dignity of the mysteries is best preserved by silence. What the uninitiated are not even allowed to look at was hardly likely to be publicly paraded about in written documents.
Basil even likened this secrecy to Moses’s tabernacle: “What was the meaning of the mighty Moses in not making all the parts of the tabernacle open to every one? The profane he stationed without the sacred barriers; the first courts he conceded to the purer; the Levites alone he judged worthy of being servants of the Deity.” This notion of liturgical practices come from a secret tradition was labeled the disciplina arcani in the early modern period.
The baptismal liturgy had a number of similarities to the temple liturgies of the apocalypses. The baptismal initiate would remove his or her old clothes, be anointed, get baptized, and receive a garment that he or she would wear for seven days. Furthermore, the Eucharist was secret in the early church: only the baptized were allowed to watch.
Augustine, in particular, worked to eliminate any notions of an esoteric doctrine for particular Christians, argues Stromousa. In his Sermons on the Gospel of John, Augustine warned against curiositas, the desire to know more than God would have us know. One can learn God’s higher truths, but one should not take short cuts by means of wicked teachers and their secret teachings. For Augustine, mystery meant sacrament. Argues Stromousa, “In its metaphorical use, then, musterion came to mean exactly the opposite of its original meaning: it is the outward expression of the divine depth, which remains unattainable.”
Protestants, who followed Augustine on many points, argued that the disciplina arcai was a later corruption that Christians adopted from the rites of the Greek mysteries.
 Morton Smith, Clement of Alexandria and a Secret Gospel of Mark (Cambridge: Harvard University Press, 1973), 283.
 Smith, Clement of Alexandria and a Secret Gospel of Mark, 283; Scott G. Brown, Mark’s Other Gospel: Rethinking Morton Smith’s Controversial Discovery (Waterloo, Can.: Wilfrid Laurier University Press, 2005), 176-78.
 Jean Danielou, Gospel Message and Hellenistic Culture, trans. John Austin Baker (London: Darton, Logman and Todd, 1973), 465-466.
 Brown, Mark’s Other Gospel, 178.
 Guy G. Stromousa, Hidden Wisdom: Esoteric Traditions and the Roots of Christian Mysticism 2d ed. (Leiden: Brill, 2005), 85, 6.
 Bernard McGinn, The Foundations of Mysticism, vol 1 of The Presence of God: A History of Western Christian Mysticism (New York: Crossroad, 1992), 99.
 Stromousa, Hidden Wisdom, 156, citing Gregory of Nyssa, Life of Moses, 2. 160-161.
 Basil, De Spiritu Sancto, chapter 27.
 “Baptism,” in Encyclopedia of Early Christianity, ed. Everett Gerguson (New York: Garland, 1990); “Alb,” Catholic Encyclopedia.
 Stromousa, Hidden Wisdom, 134-43, 163.
 Wouter J. Hanegraaff, Esotericism and the Academy: Rejected Knowledge in Western Culture (Cambridge: Cambridge University Press, 2012), 99.