When Yamato was abducted by Kabutomaru, his consciousness drifted to our real world, more especifically to Naruto Base, whereupon he discovered an enemy far scarier and more powerfully despicable than Obito and Orochimaru together: Fanboys. Led by their mastermind Organization: Uchiha Fanboys, and its head: Praise-Lord-Sasuke LOL. Yamato also discovered their nemesis, the Naruto-Minato-Hiruzen Fanboys, who consider themselves Those Who Walk in The Light, but who have proved to be as powerfully despicable as the Uchiha Fanboy Organization.
Terrified by this discovery, and sincerely hoping that someone saves him, Yamato lays defenseless, powerless in the root of Hashirama's DNA source. I feel bad for him, but hey! Soon enough, Naruto or Kakashi (who I think has sort of a gay crush on him) will save him. Rest assured.