The Bloody Mist attacking Kakashi and Rin was a setup and the mastermind behind all this is Uchiha Madara! Yes the real one, the old fart that we saw in chapters 603-604, but how?
It was said I think by Kisame or Mei that the 4th Mizukage was being controlled during the time when the Mist village was called the Bloody Mist. "It couldn't be Madara because the 4th Mizukage looks too young to be alive by that time" You may think that but, the 4th Mizukage if he didn't die when he died I say that he would be as old as Onooki! The Sambi didn't have a Jinchuuriki when the Akatsuki captured it, that means that Yagura had to die a while ago for the Sambi to revive. Yagura died young, thats why Edo Yagura is young.
I don't know how Madara was controlling the Mizukage from his hideout but he was! When you look at this panel
You can't see any dead bodies! That means that theres only Kakashi and Rin that are from the Leaf, the rest of all those shinobis are from the Bloody Mist, Kakashi and Rin were alone and were out of nowhere ambushed by this anemies. But why so many? Because this was very important for Madara to abduct Kakashi and Rin to brainwash Obito.
How did Madara know about Rin and Obito? Obito was yelling their names when he was asleep and he talk to Madara that he was going to leave he's cave to be with them! (If Madara gets rid of both of them then Madara doesn't have to worry of Obito wanting to leave)
Here ^ he tells Madara why he want to leave.
Here ^ he reveals who they are.
So back to Chap 605 when they guy from the Bloody Mist says "At least retrieve the woman"
They thought Kakashi was dead so there is no need to take him back, IMO Rin is still alive but is at the brink of death!
After revealing Tobi's identity was Obito, after revealing that Obito survived being crush by a rock was by slipping a lil bit and ending in Madara's hideout, you cannot think too far outside the box, so I will say that Rin was under a Zetsu's jutsu so she could look like an enemy. Just like a substitution jutsu when you attack it, it poofs after a sec and it is just a piece of wood, when Kakashi speared this "enemy" it turned out to be that that was Rin! That's why he was crying after he realized that he, himself killed Rin, Zetsu brings Obito to the scene at the perfect moment so Obito couldn't see what really happened!
Also by Madara being so confident that Obito will return back! It shows that this is 100% Madara behind this! Even though by my theory it makes it sound like Madara had to go to a plan B to brainwash Obito, he was successful doing it.
You may be wondering why I bolded Bloody Mist. Well When Madara was controlling the Mizukage, that's when the village was called like that, here the enemi says "Don't understimate the Village of the Bloody Mist
Madara is behind everything.
Maybe after that happened Madara or Zetsu told Obito what really happened but at that time is too late so he just kept going with the plan. I say that Obito learned the truth of those events because here, Obito's doesn't credit Kakashi for the kill, he says "You let Rin die"
Thanks for your time.