Onoki was given a request by the Raikage to attend a Kage summit in the Land of Iron, and part of the summit's clause is that he can only bring two bodyguards and that; he chose Kurotsuchi and Akatsuchi to go with him. Akatsuchi shows great concern for Onoki and offers to carry his luggage when his back gives out, Kurotsuchi however hassles Onoki for being too stubborn to retire and choose a successor. On the way to the Land of Iron, they asked him about where they were going and he explained that the Land of Iron is a neutral country but has a powerful military consisting of Samurais rather than Ninjas.
At the Kage summit, Onoki was a bit of a trouble maker, giving everyone a hard time, especially Gaara. Here it was revealed that Onoki had used Akatsuki many times in the past, and blamed the Raikage for needing to do so since the Cloud village had been increasing their military power. When it was revealed that Danzo was trying to manipulate the vote to become the leader of their alliance, he and Danzo had a small conversation. Danzo explained that Hashirama united the clans to form the villages to stabilize the lands, and now he's trying to bring together the villages to stabilize the world, a world that Akatsuki threatens to destroy and he has to stop. Onoki told him that ideals take time to flourish and that he should had been more patient because in his haste, despite his good intentions, had only succeeded in created mistrust and hate. Danzo replied that he doesn't care what anyone thinks of him as long as something gets done. Onoki himself however was put in his place by Gaara.
While Raikage and his body guards were off fighting Sasuke, Kurotsuchi wanted to go watch since Sasuke was the one that killed Deidara, but Akatsuchi opted to stay behind and tend to Onoki. Sasuke eventually found himself in the Kage's room and Mizukage said she'd handle him, Onoki decided to not interfere. Zetsu however had secretly infected all of them with one of his jutsus, saving Sasuke from Mizukage. They all freed themselves of Zetsu's trap and Onoki proceeded to try to kill Sasuke, Madara however teleported in and saved the unconscious Sasuke. Madara revealed his plans to unite the world, which confused Onoki; he once fought Madara and knew first hand of what he was capable of, saying that Madara should have the power to do anything he wants and wondered why Madara was being so sneaky, to which Madara revealed that his fight with Hashirama left him weakened.
After Madara left, Onoki decided to join the alliance with the other Kages. He wanted to put Killer Bee and Naruto on the front-lines in order to combat against Madara's collection of Bijuu, however the others disagreed, saying that's what Madara probably wants so he can capture them and that they have to keep the Jinchuuriki safe. After leaving the summit, Kurotsuchi advised to kill the Jinchuurikis so that Madara couldn't get the last two Bijuu, but Onoki remembered what Gaara said to him and decided not to.
At meeting Onoki agreed that the best place to hide Naruto and Killer Bee would be in the Cloud village on their hidden island. But later when the Jinchuurikis' whereabouts are compromised, it's discussed what should be done. It's decided that only a small elite team should go as not to openly reveal their location and Onoki volunteers himself to go. Gaara tries to go himself, but Onoki insists and sets out with Kurotsuchi and Akatsuchi after giving them his ability to fly.
As Kabuto and Deidara closed in on the island turtle that Naruto and Killer Bee are on, they are intercepted by Onoki whom ambushed Kabuto and punches a hole in Kabuto's chest, but it's Deidara's clay clone which explodes. However it wasn't the real Onoki either, it was an Earth Clone made by Akatsuchi. While they're engaged, Kabuto reveals that he has made a bigger, more powerful clone of Manda which finds and attacks the island turtle. Deidara detonated some of his clay bombs beneath the island turtle trying to make it topple over, but it didn't. Kabuto went off to find Naruto and Killer Bee while Deidara kept the others busy, but Kurotsuchi chased after Kabuto. Onoki prepared to use an immensely powerful Dust release jutsu against Deidara, but is stopped by Akatsuchi whom reminds Onoki that he'd kill the island turtle. Deidara takes the opportunity to attack with a clay bomb, but Akatsuchi blocks it with one of his stone golems.
Onoki and Deidara then engage in an aerial battle, one which Akatsuchi cannot keep up with, and Onoki comments on how he always hated how Deidara would sneak off and attack. Once they're far enough away, Onoki attempts to use his jutsu again, but Deidara is unsummoned after Kabuto escapes. Onoki returns to talk to the others and they reveal that Kabuto captured Yamato. This makes Onoki unsettled but they ensure him that Yamato won't reveal any information, Onoki however replies that Yamato won't be able to resist Madara's power.
As the war progressed, news came to light that Kabuto had resurrected Muu, the Second Tsuchikage and the one who taught Onoki Dust jutsus. Both Onoki and Tsunade agreed that he was the only one who could stop Muu. During the course of the battle, Onoki strained his back too much and needed assistance from Gaara. Despite this, Muu was gaining the upperhand until one of Naruto's Shadow Clones arrived to help and they momentarily defeated Muu. Onoki and Gaara moved onto confront the 2nd Mizukage whom proved to be even more challenging, especially since Onoki didn't have enough chakra to use his Dust techniques anymore. Thanks to Gaara's cleverness, they were able to finally defeat the 2nd Mizukage. To their surprise, Muu was not yet defeat... but more shocking than that was the sudden arrival of Madara Uchiha, leaving the alliance to wonder who the masked man really is. During a short confrontation, Madara resorted to trying to wipe out all of his opponents with an asteroid. Onoki succeeded in stopping it, but was unable to stop the second one which wiped out most of the division and left him greatly injured. The arrival of Tsunade, Ei, and Mei however tipped the odds into the alliance's favor against Madara...
Onoki has shown the ability to use Earth jutsus, using a jutsu called "Rising Earth Core" to move a section of the ground up or down, "Rock Fist" where he covers his hand and arm in rocks for improved striking power, "Rock Clone" where he creates duplicates of himself using stones as a medium, "Stone Golem" in which he creates a giant humanoid statue to attack or defend. He also has "Added Weight Rock" and the more powerful "Super Added Weight Rock" which increases the weight of whatever he touches. He has shown the ability to fly by currently unknown means, and can make others fly by touching them; this could be related to his jutsus "Light Weight Rock" and the more powerful "Ultra Light Weight Rock" where he can make things lighter by touching them. He can also combine Earth, Wind, and Fire to use a bloodline limit called Dust release (Jinton). He has used one Dust jutsu so far: Detachment from the Primitive World, which destroys the molecules of whatever it hits.