Reed,
It is extremely complicated, but the basic reason is this; after the Revolution, and the assassination of the Emperor, the church was in a quandry--there was no Emperor, and therefore, no head of the Church.
The Communist government deeply restricted the influence and authority of the Orthodox Episcopate, and the Communist leaders appointed collaboratist priests who supported Communist doctrine and altered the Orthodox ritual.
Outside of Russia, loyalist and conservative Orthodox priests from the Russian tradition organized to continue the Russian Orthodox Church as it existed under Imperial authority. Since there was no clear head of the Church, a "Patriarch in Exile" was elected as head of the Church. In this period, the OCA broke away as well, as did many national branches of the Russian Church abroad (Russian Church in France, Germany, Belgium, etc. -- all Russian Churches who did not acknowledge the Soviet regime.)
During the Second World War, Stalin allowed the churches to open again, and I believe (but I'm not sure) appointed the first Soviet "Patriarch."
Since the fall of Communism, the Churches has been in a careful state of potential entente--their differences are largely political, and ocasionally financial (they argue over real estate a lot.). ROCOR feels that the Church in Russia is still filled with collaboratists, and the ROC in Moscow feels that ROCOR are traitors who abandoned the Church in its moment of need, as it struggled to exist under Soviet authority. They are both right, and they are both wrong.
Now, I may have the specifics wrong, but that is the gist.
Best,
Nick