[This comes from a comment I left on another blog a while back. The topic was the return of the Jews to Jerusalem and the work of Ezra and Nehemiah in restoring the temple.]
The Samaritans considered (and still consider) themselves to be direct descendants of the people of the Northern Kingdom. When the Jews came back to to Jerusalem the Samaritans were happy to help because they were helping their cousins. That is until Ezra came to town and told the Samaritans to take a hike. Also keep in mind that the Jews (from the Southern Kingdom) never really considered the people from the Northern Kingdom to follow the “true Church”. So the Jews thought that just about anyone from the North was apostate even before the Jews came back from Babylon.
So the first Jews who came back to Jerusalem got there and were like, “Great! More Israelites to help us!” But Ezra shows up and says, “But they are from the apostate North. And they can’t prove their lineage so we are just going to assume that they intermarried with other people and are therefore not ‘pure blooded’ Israelites.” The standard thing that is usually taught in our Sunday School classes, Institute and Seminary, is that the Samaritans were people brought in by the Assyrians or Babylonians who may have intermarried with any remnant Israelites who survived. This is partially true.
The city of Samaria (capitol of the Northern Kingdom) was largely depopulated by the Assyrians. We don’t really have a good idea on how the surrounding towns and villages were affected. I have seen articles saying that the entire north was depopulated and others say that there is no break in the archaeological record in some of the Israelite towns around that time. From what I have read there may have been a non insignificant population of real, true blooded, Israelites still living in the north when the Babylonians destroyed Jerusalem. There was also a significant population of refugees from the north living in Jerusalem at the time . For example, Lehi and his family were from that population of refugees. Either Lehi’s grandfather or great-grandfather were among the original refugees from the north.
The Assyrians also brought in other people to populate the city of Samaria and it is with these people the remainder of the Israelites in the north may have mixed. So the Israelites/Samaritans who wanted to help build the temple may have been pure blooded Israelites, mixed blood Israelites or even non Israelites. For the pure blooded Israelites (or even those who thought they were pure blooded, because we all know how sometimes we just don’t talk about (great-)grandpa’s second, or third wife or uncle Bob who married….her) to have Ezra then come in and say “Y’all ain't real Israelites.” would have been perceived as “He’s just spreading rumors to cut us out of the work being done on the temple.” (Read: He’s giving preferential treatment to his family and business cronies for all that cash flowing in from Persia).
So from stuff that I've read the Samaritans perceived it as a smear campaign based on baseless rumors (“Because, like who are they to talk. I mean, they’re all the ones coming in with their Babylonian (and Chaldean! Scandalous!) wives and dirty half breed children. Our linage is pure I assure you.”)
In response to this the Samaritans argued that the Jews who came back were not pure blooded Israelites since they intermarried with Babylonians (as evidence they would point to the Jews who had Babylonian sounding names). So accusations of infidelity and interbreeding abounded and in the end the Samaritans were kicked out off of the temple project. The Samaritans responded by going north to Mount Gezirim (you know the one where Joshua put the tabernacle after they crossed over the Jordan, except the Jews went back and edited Deuteronomy to have him putting it on a different mountain, but the Dead Sea Scrolls agree with the Samaritans on this one), and built their own temple. This one was larger and more impressive than the one in Jerusalem and got more patronage and monetary support from the Persians which is something that the Jews don’t like to mention. They don’t like people to know that Artaxerxes spent more money building the temple on Mount Gezirim than the one in Jerusalem. Also they don’t like people knowing that a Jewish/Israelite governor was also appointed in Samaria and also resettled Babylonian Jews there.
The Jews were a little jealous of the larger and more spectacular temple in Samaria and thus it was rather scandalous when the eldest son of the high priest (i.e. the next high priest) was persuaded by the Samaritan governor to come be the high priest for the temple in Samaria. Keep in mind that priesthood authority was transmitted father to son so this would have been viewed as a legitimate transfer of authority from the temple in Jerusalem to the one on Mount Gezirim. Ezra and Nehemiah were quite upset and promptly excommunicated him (and anyone else associated with him). So the Jews (and Ezra and Nehemiah) were trying to establish their legitimacy in Jerusalem while many Jews (and their money) just stayed in Babylon (“We’ll just stay put until you get your priesthood authority issues worked out.”).
The Jews considered themselves to be vindicated when Alexander the Great came through and destroyed the city of Samaria (but not the temple on Mount Gezirim), but left Jerusalem untouched. Afterwards the Jews rebelled against the Greeks and fought a few wars with them (cf. Maccabees). The Maccabees were upset that the Samaritans were getting along with the Greeks and sort of formed a tenuous alliance with a bunch of upstart warmongers from a city that no one had ever heard of called Rome. In the process the independent Jewish king took it out on the Samaritans and destroyed their temple and killed a bunch of them (like a non insignificant part of their population). They (the Samaritans) were rather upset and never forgave the Jews. So when the Romans came tromping through a few years later looking to be paid for helping the Jews out against the Greeks, the Samaritans gleefully supported the Romans and helped bolster the new “independent” and “Jewish” king named Harod, for which the Jews never forgave them.
So when Jesus told the Samaritan woman at the well (literally at the foot of Mount Gezirim), “Woman, believe me, the hour cometh, when ye shall neither in this mountain [Gezirim], nor yet at Jerusalem, worship the Father.” He meant that it didn’t matter who was right or wrong in the Ezra-Samaritan dispute because by then neither one (Jew or Samaritan) was in the right or had the authority.
So the story of Ezra is perhaps one of the more under appreciated and historically messy stories from the Bible. It is a story about priesthood authority and how that authority is transmitted correctly. History sure is a mess. And even more so when you hear every side to the story.
For anyone who is interested here is some further reading:
Who Were the Samaritans? by Taylor Halverson.
The Dating of the First Phase of the Samaritan Temple on Mount Gerizim in Light of the Archaeological Evidence, by Yitzhak Magen, found in Judah and the Judeans in the Fourth Century B.C.E.