Hi all, I'm just trying to piece together what really happend in regards to the Mormons in Missouri. I know that it can't be as one sided as the story I got in church. Any help/references would be greatly appreciated.

If you want more details, the best book, bar none, is Stephen C. LeSueur's The 1838 Mormon War in Missouri.

http://www.amazon.com/1838-Mormon-War-Missouri/dp/0826207294

One of the problems was that Sidney Rigdon on the previous July 4 had preached in a public sermon (later published as a pamphlet) the Mormons' declaration that the conflict between Missourians and Mormons would be a "war of extermination," either "them or us."
http://en.wikipedia.org/wiki/Rigdon%27s_July_4th_oration

Here are some issues that come up in discussions.

There was a lot of land speculation where ever Mormons went. Smith was very involved in buying up land and selling back to followers, presumably at a nice profit. Our own recent real estate bubble is a good example of how people get hurt by this.

The Nauvoo charter gave Mormons special legal rights. The rogues among them were free from fear of prosecution if they raided local Missouri farms.

Mormons have never been interested in doing things the way everyone else does. Just as now, it is their way or else because God told them so.

The polygamy rumors were flying. Odd sex in the local cult is a universal tip off to normal people.

Nauvoo had a huge army and JS named himself as General. He also crowned himself King and ran for US President.

They practiced block voting to get a strong foothold in local politics.

The "1838 Mormon War in Missouri" is supposed to be very fair:
http://www.amazon.com/exec/obidos/ASIN/0826207294/rpcman

it should be noted that the Nauvoo charter and Nauvoo legion came after the Mormons had left Missouri, and thus did not contribute to their problems in Missouri.

Thanks too all who responded! I'll be getting the book.

Fawn Brodie's book goes over this fairly succinctly. Besides the issues above, the Mormons weren't entirely innocent in provoking others by sending groups to harass others (even if they didn't always do anything, the idea would be frightening to a normal person).