Sanhedrin 12a: The Sages say that Beis Din should not add an extra month to the year to allow time for tamei people to become clean before Pesach, but rather they should make Pesach with tumah. Rabbi Yehuda disagrees and holds it is better to add the month. And this was the story with Chizkiyah, king of Yehuda: he added a month due to tumah.
Tosafos: What was the tumah in the case of Chizkiyah? The Yerushalmi says that they found the skull of Aravna the Yevusi under the mizbeyach.
סנהדרין יב ע”א: תנו רבנן: אין מעברין את השנה מפני הטומאה, רבי יהודה אומר: מעברין. אמר רבי יהודה: מעשה בחזקיה מלך יהודה שעיבר את השנה מפני הטומאה. תוס’: ובירושלמי אמר דגולגלתו של ארונה היבוסי מצאו תחת המזבח.
After the shaitel controversy in 2004, Rabbi Ahron Dovid Dunner went to Rabbi Chaim Kanievsky and asked, “Sometimes it happens that there is a ‘tummel’ and we find out that everyone has been doing something wrong for a long time. Is there a precedent in Chazal for such a thing?” R’ Chaim replied, “The Yerushalmi says that they found a skull buried under the mizbeyach.” That meant all the avodah in the Beis Hamikdash for the last 300 or so years had been invalid and forbidden. You can’t imagine more of an upset than that.
[The Tzion Yerushalayim (on the page of the Yerushalmi Pesachim 64a) asks that Aravna was a non-Jew and we hold that the graves of non-Jews are not metamei. He says to look in the Mishneh Lamelech on Beis Habechirah 1:13. There the Rambam writes:
המזבח אין עושין אותו אלא בנין אבנים גזית וזה שנאמר בתורה מזבח אדמה תעשה לי שיהיה מחובר באדמה שלא יבנוהו לא על גבי כיפין ולא על גבי מחילות.
“The mizbeyach must be built of hewn stones. And although the Torah says, ‘You shall make Me an altar of earth,’ that does not mean that the actual mizbeyach should be made of earth, only that it must be connected to the earth, not built atop domes or tunnels.”
The source for this Rambam is the Gemara in Zevachim 58a. The Mishneh Lamelech points out that we see here that the mizbeyach was different from all other areas of Har Habayis, which were in fact built on top of underground domes to prevent any tumah from coming up. This is stated by the Rambam in Hilchos Parah Adumah 2:7:
שכל הר הבית והעזרות תחתיהן היה חלול מפני קבר התהום.
And his source for this is the Mishnah in Parah 3:3.
The Mishneh Lamelech says that now that we have established that there was no separating dome under the mizbeyach to block the tumah, we understand why it was such a problem when they found the skull of Aravna the Yevusi.
The question is: Dovid bought the field from Aravna when he, Aravna, was still alive, so how could he have been buried there? And even if we say that David let Aravna continue to live there until the Beis Hamikdash was built, why would he have been allowed to be buried there, given that they were planning to build the Beis Hamikdash?
In Makos 11a we read the story of how Dovid Hamelech dug the Shisin (the tank under the mizbeyach into which the wine of the nesachim ran). Water from underground began spraying upward in a geyser, and he asked Achisofel whether it was allowed to write the name of Hashem and block the hole. Rashi asks: Achisofel died during the rebellion of Avshalom, three years before Dovid bought the Temple Mount. He answers that many years earlier Dovid had already figured out with Shmuel where the Beis Hamikdash would be, and he dug the Shisin with permission from Aravna.
Accordingly, it may be that Aravna fell into the Shisin, which was already dug in his time, and died. The kohanim in Chizkiyahu’s time perhaps discovered it when they went down to clean the Shisin. The Gemara says (Meilah 11b) that once in 70 years, the young kohanim would go down into the Shisin and clean it out. Maybe this was not yet done regularly during the First Beis Hamikdash era.
Why wouldn’t the empty space in the Shisin be a separation to stop the tumah from going up? Maybe it was originally, but after it became full of dried up wine the space was filled.
Based on Pesachim 81b, the tzitz atones for tumah of the tehom – tumah that no one knows about. If so, we have two reasons to argue that all the offerings brought before Chizkiyah’s time were not invalid: 1) The Shisin originally had a hollow space above the skull, 2) The tzitz atoned.
If there is a rule that the mizbeyach must not be built over empty space, then why was it allowed to have the Shisin? The answer may be that only man-made domes are forbidden, but the Shisin was a natural cave, created in the six days of creation (Succah 49a) and all Dovid Hamelech did was clear out the loose dirt and pebbles from it (Rashi Succah 53b).
Today there is a cave under the rock in the Dome of the Rock. Rabbi Leibel Reznick has proposed that the rock, as the original peak of the mountain and the only place there not built on domes, is the place of the mizbeyach. The cave under it would then be the Shisin. There is a large, round marble slab on the floor of the cave, and it is said that this slab covers the entrance to another cave below. The Radbaz writes (Teshuva 691) that he heard from Arabs that the earlier kings wanted to see what was in the cave, so they lowered people down, and they died. (Presumably the people who died were pulled back up, so we won’t have to worry about skulls down there when moshiach comes.) Therefore they closed off the cave and filled it with dirt, and to this day no one knows what is there.
In 1865 Captain Charles Wilson was sent with the sanction of the British War Department to survey the water supply of Jerusalem. The director of his survey writes that the hole in the bottom of the cave leads to a drain flowing down to Nachal Kidron. The Mishnah (Midos 3:2 and Yuma 5:6) indeed says that the blood flowed down from the base of the mizbeyach into a drain leading to Nachal Kidron.]
Source: Tape by Rabbi Ahron Dovid Dunner; The Holy Temple Revisited by Leibel Reznick p. 113