Yamato is most likely dead. Sorry did I ruin your party? Ok I'll change it then.
Yamato has escaped from Tobito's hideout and will rendezvous with Naruto and company at the battle field. Upon seeing that Naruto has complete control of the Kyuubi, he'll realize that one of the fundamental reasons for even creating and introducing his character is now null and void making him near useless.
He'll take some solace in the thought that he can still use his wood jutsu to make large scale attacks, and attempt
to put all his chakra into creating a powerful wood jutsu that might
wrap around the 10-tails legs strong enough to immobilize it. Instead a massive forest will erupt from the ground, that completely wraps around the 10-tails, engulfing every inch of the monster is an endless see of trees and vines, that despite it's godly strength it can't even budge an inch from. Yamato will be all like "fuck yeah, I'm awesome", until he looks to the very top branch of the highest tree and sees Hashirama standing there looking down on him with a troll face smile.
Upon realizing the other
reason his character was remotely mentionable is now also invalidated, Yamato takes off his ninja headband, throws it to the ground and leaves the battlefield and his ninja life behind. He sets off on a long overdue journey to fulfill his lifetime goal of becoming the greatest pornstar to ever live. Believe it. After Yamato, who goes by the name "Mr. Wood" in the business, has produced more videos than the amount of missions he ever went on, he becomes famous throughout the land. Pervs look up to him, Playa's envy him, and Milfs lust after him. He then auditions for the show Konoha's Got Talent as a musical act, and ends up winning. He goes on to make numerous albums including what many call his greatest hit Wood
. He goes on to host his own successful TV show, that runs for many years, replacing Dr. Phil, to which every rejoices. Later on, in the twilight of his life, he gets called back into ninja service when he's asked to moderate peace talks between the Leaf and Cloud villages. At the conference he uses his wood jutsu to grow a batch a marijuana for his cataract pains, which also unexpectedly helps broker decades of peace between the 2 villages. A large statue is erected in his honor in the shadow of the Hokage mountain. Yamato later finally dies at the ripe old age of 96, surrounded by his family, friends, and of course vast fortunes.
Sadly a few years after his death his past catches up with him. Shortly after his death when his body started to decay, many of the dozen or so STD's he acquired over his long porn career began to mingle with each other and the decaying flesh and as a result mutated exponentially. All it took was for one lone grave robber to break open his casket and the disease, now airborne, spread across the continent killing 95% of the human population in mere weeks. Many people fled to the mountains to escape the plague, and in the coming decades saw their society degenerated into a mere shadow of it's former self, forgetting most of their ninja training, and becoming mere wandering nomads that lived a tribal life.
Many centuries would then pass, before a group of explorers from a far off continent would come on a expedition to these new lands. Led by a man named Amerigo Vespucci, they surveyed the ancient ruins of Konoha, collecting evidence of the civilization that once thrived there, and the "magic" their shamans were supposedly capable of. Upon finding a book named the "Yama Sutra", and seeing the statue of the man depicted in the book under the mysterious faces on the mountain, archeologists can only conclude the being named Yamato must have been the god of fertility for the native patheon.
So ends the life and legend of one of konoha's finest.