Matt stopped running for a while after reaching a cave to rest.
Alice had fallen unconscious a while ago, although Matt didn't understand why. The wounds on her body were not too serious to lead to unconsciousness. So, it was possibly some internal struggle.
Still, it gave him time to think about the things that had happened recently.
The Charlotte thing had become clear to him. Her plan was to lead the human race to certain extermination.
She is a great strategist; she has many ways to do it without them realizing it. He has full confidence in her abilities to do so, so he is not worried about her.
But he also knows that doing so is too dangerous. One wrong step could cause her to become the primary enemy of the human race. That is why he must become strong again.