In Temple times, the weeks leading up to Pesach included not only preparing the house but the body as well, for anyone who had contracted corpse-tumah had to purify themselves before partaking of the Pesach offering or visiting the Temple. The procedure entailed a one-week quarantine during which the individual was sprinkled with spring water mixed with the ashes of the red cow [parah adumah]. It was not necessary to travel to Jerusalem to do so but rather this could be carried out in the comfort of one's own city since the family groups [mishmaros] of Kohanim living throughout the land of Israel possessed small, but sufficient, amounts of ashes for this express purpose.
It once happened in the First Temple era during the reign of King Chizkiah that an unprecedented breach of ritual purity caused the festival of Pesach to be delayed a full month (Sanhedrin 12a). One theory as to the source of this tumah is that the skull of Aravnah the Jebusite was discovered beneath the Altar (Tosafos ad loc., based on Yerushalmi Sotah 5:2). [Aravnah was the owner of the threshing floor purchased by King David to serve as the site of the future Temple (II Samuel 24:18-25).]
There are a number of difficulties with this approach:
1) If it was a matter of corpse-tumah, the purification procedure only takes one week, so why was a whole extra month needed?
2) If the remains of Aravnah were causing the tumah, could they not simply be removed from the Temple precincts (where they obviously did not belong) and reinterred elsewhere?
3) Why is it that the skull was only discovered at this point?
4) A closer look at the source in Yerushalmi indicates that this incident of the skull being found occurred in the Second Temple era, not the First Temple era (as Tosafos understand).
The Chasam Sofer (to Sanhedrin 12a) offers a novel historical perspective which addresses each of the above questions. When Aravnah sold his threshing floor to King David he reserved a small portion of his estate for himself and it was there that he was eventually buried. In that region of Jerusalem there were many natural subterranean tunnels and the tumah from Aravnah's tomb made its way through them to the area beneath the Temple. Now, when the First Temple was built King Solomon had taken this into account and he designed the walls in such a way to form a halachic barrier to the tumah which kept it from invading the Temple grounds.
Many years later, the evil King Achaz destroyed the original Altar and built a new one for idol worship in its place, and the extent of his "renovations" was such that it disrupted the halachic barriers put in place by Solomon. When King Chizkiah took office and began to repair the Temple, the tumah from Aravnah's tomb was rediscovered. [Although the Gemara speaks of Aravnah's "skull," Chasam Sofer explains that the term גלגל actually refers to the spreading of tumah underground. See further there.] The remains could not be moved since they were in their rightful place so Chizkiah needed to repair the halachic barriers in order to ready the Temple for use. This, however, was not a simple matter, and he found it necessary to delay the festival of Pesach by one month in order to allow his men time to carry out the repairs.
When the First Temple was destroyed by the Babylonians they razed the building down to its very foundations ["aru, aru, ad hayesod bah"], once again breaking down the barriers which shielded the Temple from the tumah of Aravnah's tomb. The Yerushalmi which indicates that the skull was discovered during the Second Temple era is describing what happened when the Temple was rebuilt by the returnees of the Babylonian exile when they once again had to address the issue of Aravnah's remains.
(Special thanks to R' Nechemiah Feldman for bringing this Chasam Sofer to my attention.)