The mishna is referring to a case where the person did not repent and persists in his rebellion, and it is in accordance with the opinion of Rabbi Yehuda HaNasi, that even for such a case Yom Kippur and the scapegoat will atone. As it is taught in a baraita: Rabbi Yehuda HaNasi says: For all transgressions that are stated in the Torah, whether one repented, or whether one did not repent, Yom Kippur atones, except for one who divests himself of the yoke of Heaven, by denying God’s existence, and one who reveals facets of the Torah that differ from its true meaning, and one who nullifies the covenant of circumcision of the flesh. For these, if one repented, Yom Kippur atones, and if not, Yom Kippur does not atone.

The Gemara asks: What is the reasoning of Rabbi Yehuda HaNasi? It is as it is taught in a baraita in interpretation of the verse: “For he scorned the word of the Lord and nullified His commandment; that person will be cut off [hikkaret tikkaret], his sin is upon him” (Numbers 15:31): “For he scorned the word of the Lord”; this is referring to one who divests himself of the yoke of Heaven and one who reveals facets of the Torah that differ from its true meaning. “And nullified His commandment”; this is referring to one who nullified the covenant of circumcision of the flesh. The use of the double verb form hikkaret tikkaret teaches that he will be cut off, i.e., he is liable to receive karet, before Yom Kippur, and he will still be cut off after Yom Kippur, as Yom Kippur does not atone for him.

One might have thought that this applies even if he repented. To counter this, the verse states: “His sin is upon him,” by which God indicates: I said that Yom Kippur does not atone for these sins only when his sin is still upon him, as he did not repent. It is apparent from this baraita that it is only for the three sins mentioned that Yom Kippur does not atone without repentance, but Yom Kippur atones for other sins even if one did not repent.

And with regard to the Rabbis who disagree with Rabbi Yehuda HaNasi, how do they interpret the verse? If someone commits one of the three sins mentioned, then he is cut off [hikkaret] from life in this world, and he will be cut off [tikkaret] in the World-to-Come. The phrase “His sin is upon him” teaches that if he repented and died, his death cleanses him of his sin.

The Gemara asks: And can you interpret the mishna to be in accordance with the opinion of Rabbi Yehuda HaNasi? But from the fact that the latter clause is in accordance with the opinion of Rabbi Yehuda, by inference, the first clause is also in accordance with the opinion of Rabbi Yehuda, but not of Rabbi Yehuda HaNasi, as the latter clause of the mishna teaches: Israelites and priests and the anointed priest, i.e., the High Priest, all equally achieve atonement from the scapegoat. And who accepts this reasoning? Rabbi Yehuda, as the Gemara will demonstrate. By inference, the first clause is also in accordance with the opinion of Rabbi Yehuda, not of Rabbi Yehuda HaNasi.

Rav Yosef said: It is possible that the entire mishna is in accordance with the opinion of Rabbi Yehuda HaNasi, and the latter clause does not pose a difficulty, because with regard to whether priests achieve atonement through the scapegoat, he holds in accordance with the opinion of Rabbi Yehuda.

Abaye said to him: Does the Master mean specifically what he is saying, i.e., that Rabbi Yehuda HaNasi holds in accordance with the opinion of Rabbi Yehuda with regard to whether the scapegoat atones for both Israelites and priest, but Rabbi Yehuda does not hold in accordance with the opinion of Rabbi Yehuda HaNasi with regard to atonement for one who did not repent? Or perhaps from the fact that Rabbi Yehuda HaNasi holds in accordance with the opinion of Rabbi Yehuda, it follows that Rabbi Yehuda also holds in accordance with the opinion of Rabbi Yehuda HaNasi, but the reason that Rav Yosef did not make this clear is that he teaches the matter in the manner in which it typically occurs, which is to say that a disciple, in this case, Rabbi Yehuda HaNasi, holds in accordance with the opinion of his teacher, i.e., Rabbi Yehuda.

Rav Yosef said to him: Yes, I mean specifically what I was saying: Rabbi Yehuda HaNasi holds in accordance with the opinion of Rabbi Yehuda, but Rabbi Yehuda does not hold in accordance with the opinion of Rabbi Yehuda HaNasi.

As it is taught in a baraita recorded in the Sifra: One might have thought that Yom Kippur would atone for those who repent and for those who do not repent, and this assertion is supported by the following logical inference: Although it would appear that since a sin-offering and a guilt-offering atone and Yom Kippur atones, it should follow that just as a sin-offering and a guilt-offering atone only for those who repent, so too, Yom Kippur atones only for those who repent, this comparison is flawed. One can claim: What is notable about a sin-offering and a guilt-offering? They are notable in that they do not atone for intentional sins like they do for unwitting sins. Can you say the same about Yom Kippur, which does atone for intentional sins as it does for unwitting sins?

The baraita continues: Since it is the case that the atonement of Yom Kippur is more far-reaching in that it atones for intentional sins as it does for unwitting sins, it follows that it should atone both for those who repent and for those who do not repent. To counter this, the verse states: “Yet on the tenth day of this seventh month it is Yom Kippur” (Leviticus 23:27). The word “yet” serves to divide and limit the atonement of Yom Kippur in that it atones only for those who repent.

Rav Yosef attributes the baraita to Rabbi Yehuda: Whose opinion is expressed by the unattributed baraitot in the Sifra? Rabbi Yehuda. And he says: For those who repent, yes, Yom Kippur atones, but for those who do not repent, Yom Kippur does not atone.

The Gemara asks: But raise a contradiction, setting one unattributed baraita in the Sifra, i.e., the one just cited, against another unattributed baraita in the Sifra, as in another baraita there it is taught: One might have thought that Yom Kippur would atone only if one fasted on it and declared it a holy convocation and did not perform labor on it. From where is it derived that even if one did not fast on it and did not declare it a holy convocation and performed labor on it, that it still atones? The verse states: “Yet on the tenth day of this seventh month it is Yom Kippur” (Leviticus 23:27). The additional emphasis on “it is” serves to teach that the day atones in any case. This baraita contradicts the one cited above that states clearly that Yom Kippur atones only for those who repent.

Abaye said: This is not difficult: This second baraita is in accordance with the opinion of Rabbi Yehuda HaNasi, and that first baraita is in accordance with the opinion of Rabbi Yehuda.

Rava said: Both this baraita and that baraita are in accordance with the opinion of Rabbi Yehuda HaNasi, who holds that Yom Kippur atones for those who do not repent, but even Rabbi Yehuda HaNasi concedes that with regard to avoiding the punishment of karet incurred for violating the day of Yom Kippur, Yom Kippur atones and one is not liable to be punished with karet only if one repented for the sin of violating the day of Yom Kippur. Perforce he must concede this point, as if you do not say so, then according to Rabbi Yehuda HaNasi, there would be no instance in which one would be liable to be punished with karet for violating Yom Kippur.

The Gemara questions this proof: Why not? You could find it in a case where he performed labor on the night of Yom Kippur and died that night, as in such a case, the daytime of Yom Kippur, which is the part of Yom Kippur that effects atonement, never came to atone for him.

Rather, say that Rava’s proof is as follows: