The whole eye link thing between Kakashi and Obito in the last chapter was bad story structure. A plot hole. I have to agree with Sawyer.
http://youtu.be/xDRFLbsjwqM
Anyway, so Nagato and Itachi were both tricked by Obito according to this chapter. Obito does all this under the alias of Tobi for a girl that didn't like him. Now we don't know if Rin was a Mist spy like Kabuto was a spy. If she was in fact a spy then she was probably faking her feelings while in the Leaf, which would make Obito look like a bigger ass for doing what he did.
Okay, Kishi, hit us with Kakshi's side of the story.