Let me clear some things up.
Kakashi was fighting Pain, who can pretty much control his own gravitional force, and repel and attract anything around him. After wailing on Kakashi and Chouji's father, he rendered both immoble. Kakashi was pretty drained of Chakra. Pain sent a nail flying at Kakashi's head, that WOULD have killed him, but he used his mangekyou at the last second to save himself. At this point, he was pretty much out of chakra, in a really bad position.
He and Chouji's father told Chouji to go report Pain's abilities to the Hokage, and sent him off running. One of Pain's clone-things sent a rocket after Chouji, which was have easily killed him. Kakashi, with the last of his chakra, chose to use his Mangekyou once more, using up all of his chakra, to make the rocket disappear and save Chouji. It worked, and Kakashi died due to chakra exhaustion...the same thing that happened with Itachi.
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