Pope Francis would absolutely baptize an alien from Mars, if one showed up at the Vatican and asked for it. During his weekly homily on Monday, Franics said that aliens — which he imagines could be "Green, with that long nose and big ears, just like children paint them" — should be baptized just like anyone else who asks for it, because it's not up to any human to decide who should receive the Holy Spirit. In other words: if God prompts some Martians to come to Earth, find the Pope, and say "we want in on this Catholicism thing." The pope would probably say "OK. cool." But probably in Latin.
Francis laid out the hypothetical situation as part of a discussion of the early Church's baptizing of Gentiles. Basically, the earliest Church contained some tension over whether there was any difference between the very early Jewish followers of Christ, and Gentiles who converted from paganism to Christianity, who would be considered "unclean" by the standards of Jewish law. Peter eventually persuades his followers that everyone is open to becoming Christian by saying, "If then God gave them the same gift He gave to us when we came to believe in the Lord Jesus Christ, who was I to be able to hinder God?"