Parts of this taken from the Catechism of the Catholic Church and from Catholic Answers. Sorry, this is rather lengthly but answers some of your misunderstandings, much like as Nicodemus misunderstood it as "again".
Scripture indicates three times when Jesus might have instituted his baptism. First, in his words to Nicodemus: “Truly, truly, I say to you, unless one is born of water and the Spirit, he cannot enter the kingdom of God” (John 3:5). Jesus seems to indicate the necessity of baptism here, but it could be that he speaks of an eventual necessity because his sacramental baptism had not yet been instituted. He speaks later of eventual necessity when he says, “Truly, truly, I say to you, unless you eat the flesh of the Son of man and drink his blood, you have no life in you” (John 6:53). Since the sacrament of Holy Communion would not be instituted until the Last Supper, his words here cannot indicate a current necessity. Similarly, when he speaks to Nicodemus it is not clear that Jesus has yet instituted the sacrament of baptism.
we see another possibility: “Jesus and his disciples went into the land of Judea; there he remained with them and baptized. John also was baptizing at Aenon near Salim, because there was much water there; and people came and were baptized. . . . Now when the Lord knew that the Pharisees had heard that Jesus was making and baptizing more disciples than John (although Jesus himself did not baptize, but only his disciples), he left Judea and departed again to Galilee” (John 3:22-23, 4:1-3).
It is generally understood that the baptisms mentioned in this passage were not yet Jesus’ sacramental baptism. For example, a footnote in the Revised Standard Version Catholic Edition Bible identifies them as “a baptism like that of John. The time for baptism ‘in the Spirit’ had not yet come.” Similarly, A Catholic Commentary on Holy Scripture states that it is “more probably not that baptism which was to give the Spirit, 7:39, but rather a preparatory rite like that of John.” Note the reference here to the later verse 7:39, which states, “As yet the Spirit had not been given, because Jesus was not yet glorified.” This verse seems to indicate that sacramental baptism would not arrive until after the Resurrection.
The third possible reference to the institution of the sacrament of baptism is found in the words of the great commission given by Jesus after the Resurrection: “Now the eleven disciples went to Galilee, to the mountain to which Jesus had directed them. And when they saw him they worshiped him; but some doubted. And Jesus came and said to them, ‘All authority in heaven and on earth has been given to me. Go therefore and make disciples of all nations, baptizing them in the name of the Father and of the Son and of the Holy Spirit, teaching them to observe all that I have commanded you; and lo, I am with you always, to the close of the age’” (Matt. 28:16-20).
If the sacrament of baptism was not instituted until after the Resurrection, Dismas’ [ thief on cross with Christ] salvation would not be subject to its current necessity. But scholars do not agree on when the sacrament was instituted, so whether or not it was necessary at the time of the Crucifixion remains an open question, as does the question of whether or not Dismas had been baptized.
That said, some will point out that it seems that at least the apostles had received sacramental baptism by the time of the Last Supper, since baptism is the “gateway” to the other sacraments (CCC 1213) and they received the sacraments of holy orders and Holy Communion that evening. We could argue that Jesus was free to administer the sacraments in any order he chose, for “God has bound salvation to the sacrament of Baptism, but he himself is not bound by his sacraments” (CCC 1257). But let’s consider that the sacrament might have been instituted before the Crucifixion.
If Jesus did institute baptism before the Crucifixion, and Dismas [Dismas was the name of the thief on the cross with Jesus] was baptized, then there is no conflict with the doctrine of the necessity of baptism. But if Dismas wasn’t baptized, does this pose a conflict? Actually, it doesn’t. While baptism is the ordinary means of baptismal graces, the Church holds that there are other extraordinary means that suffice when certain circumstances exist. One of those is baptism of desire. The Catechism explains:
Since Christ died for all, and since all men are in fact called to one and the same destiny, which is divine, we must hold that the Holy Spirit offers to all the possibility of being made partakers, in a way known to God, of the Paschal mystery. Every man who is ignorant of the Gospel of Christ and of his Church, but seeks the truth and does the will of God in accordance with his understanding of it, can be saved. It may be supposed that such persons would have desired Baptism explicitly if they had known its necessity (CCC 1260).
So it could be that Dismas [thief on cross with Jesus ] was ignorant of certain things but he experienced a true conversion on his cross and was saved because he would have desired baptism had he known. Or maybe he wasn’t ignorant but he had not yet had the opportunity for baptism and his actual desire for it sufficed: “For catechumens who die before their Baptism, their explicit desire to receive it, together with repentance for their sins, and charity, assures them the salvation that they were not able to receive through the sacrament” (CCC 1259).
Whatever the case may be, Jesus’ words on the cross to Dismas [thief ] do not contradict the doctrine of the necessity of baptism as the Catholic Church teaches it.
