[Barnes]

So, last year they introduced time travel. This year they have introduced alternate/paralel realities. We get to see what happens to the passengers of the Oceanic flight through the flash sideways. The temple is a gateway to another alternate universe where the Japanese guy and his crew live. I think that Richard is from this reality and went to the lost reality to observe for the Japanese guy. The guy living on Lockes body/smoke monster was at one time trapped in jacob's cabin when it was encircled in ash but someone broke the ash circle and he escaped. When he was out, he began to set his plan in motion to kill Jacob by using Christian Shepards body to talk to Ben and Locke.

The smoke monster/Locke is trying to get back to the Japanese guys reality to rule an enslave the people there. I am guessing that Jacob and Locke/smoke monster did battle in the Japanese guys reality but where sent to the lost reality where they could no longer fight each other but at least Jacob was able to keep Locke / smoke monster from doing any harm.