Several questions arise over the baptism of Helam by Alma. First, where did Alma get his authority. President Joseph Fielding Smith responded to this question:
In the case of Alma and his priesthood, we are left to surmise that he legally and divinely received it before the days of King Noah. We read that Zeniff, the father of Noah, was a righteous man. Alma evidently received the priesthood in the days of Zeniff, and at no time did he fully accept the teachings nor with full purpose to follow the counsels and procedures of Noah and his wicked priests. It was Alma who was deeply touched at the scathing denunciation of the Prophet Abinadi. Moreover it was Alma who recorded them, for he believed thoroughly in what Abinadi had declared and he turned from whatever transgression he had committed and set forth with a repentant spirit to gather together all those who were willing to accept the teachings of the martyred prophet.
Secondly, why is the baptismal prayer different than the set prayer given in the Book of Mormon when Christ visited the Nephites (3 Nephi 11:25–26) or in the Doctrine and Covenants? (20:73–74). Alma was one of the priests of Noah who had gone into apostasy. He may not have known or remembered the prayer and so used the prayer to the best of his memory. He did have the essential parts: the authority from God and the method of immersion. The last part of the prayer seems to be more of a blessing that was added to the prayer. It should be remembered that “the Spirit of the Lord was upon him as he baptized Helam.”
Thirdly, why did Alma immerse himself with Helam? This question was also answered by President Smith:
If he [Alma] had authority to baptize that is evidence that he had been baptized. Therefore, when Alma baptized himself with Helam that was not a case of Alma baptizing himself, but merely as a token to the Lord of his humility and full repentance. In Alma 5:3 we learn that Alma [the younger] was consecrated the high priest over the Church under his father. Now Alma did not organize the Church with the idea that they had no church before that time. They had a church from the days of Lehi and Alma only set things in order.
The two hundred and four souls who were baptized were called the Church of God, or the Church of Christ (Mosiah 18:16–17). There is no mention of the Church being organized. This implies, as President Smith said, that “Alma only set things in order.” In further support of this statement, when Mormon was abridging the record of Third Nephi, he said Alma established “the first church which was established among them after their transgression” (3 Nephi 5:12; emphasis added). It should be remembered that at this time Mosiah was a prophet, seer, and revelator in the land of Zarahemla (see Mosiah 8:13–17). We will read later that Ammon, who came from the land of Zarahemla, declined from baptizing the people of Limhi, not because he didn’t have authority, but because he considered “himself an unworthy servant” (Mosiah 21:33). There was indeed a Church and the priesthood among the main branch of the Nephites.