The reference to Allogenes is quite an enigmatic one in the Gospel of Judas. In the Nag Hammadi corpus, there is a tractate entitled Allogenes which relates the story of how "Allogenes" gradually attained true gnosis (particularly relating to the Triple Power of Being, Vitality, and Mind, a concept influenced by Neo-Platonism) and divinity and how he has returned to instruct a neophyte named Mesus to follow his own example. Porphyry (Vita Plotinus, 16) in the third century also mentions the use of "the revelations bearing the names of Zoroaster, Zostrianus, Nicotheus, Allogenus, Mesus, and others" by heretical Christians. The character of Allogenes in the Gospel of Judas raises the question of relation between Judas and these other Sethian treatises (including the Apocryphon of James, which Allogenes is dependent on, and Zostrianus, which was included alongside Allogenes in the Nag Hammadi library), and it raises the question of who Allogenes was supposed to be in the plot of Jesus' betrayal. The pages are out of context, so I have no idea whether Allogenes is a name used of Christ, or Judas, or someone else entirely.
The extant story here seems to start with the humiliation of Allogenes; if there is continuity in pronominal reference, Allogenes would seem to no longer "have the power to enslave them", whoever "they" are, they are now "victorious" over him. In connection with the passion, this language sounds suggestive of Christ's humiliation of the archons (cf. Colossians 2:14-15; 1 Corinthians 2:7-8; Ascension of Isaiah 10:7-12; compare also John 12:31-32, 14:30, 16:11, 33 in which Jesus has condemned the "prince of the world" and "conquered the world"), and is reminiscent too of Irenaeus' (Adversus Haereses, 1.31.1) statement about throwing heavenly things into confusion. Could this mean that Allogenes is an archon? Then Allogenes prays to God for deliverance, and the prayer is reminiscent of Jesus' prayer to his Father on Mount Olives just prior to his betrayal (cf. Luke 22:42, "If you are willing, take this cup away from me"). Then we read that a cloud of light surrounds Allogenes (curiously, there is a shift to the first person here), and a voice addresses him: "O Allogenes, the voice of your prayer was heard and I was sent to you into this place to tell you the good news". But he recognizes that this is not the God of the "highest aeon" and Allogenes declares him to be Satan and commands him to flee from him, for "it is not you I seek but my Father". That sounds a lot like Jesus, but could it have been spoken by an archon, or by Judas? Considering Allogenes' role in the Sethian corpus as a revealer of true gnosis, it is hard to picture him on the side of the archons, and yet he appears to have been humiliated and lost power. As to his own identity and name, Allogenes declares to Satan, the "one who rules the world": "I am from a different race (genos). I am not of your race". This adds to the mystery. Is Allogenes different because he is man? Is he different because he is not an archon? Is Allogenes Judas? I guess time will tell.