Naruto, enraged by the actions of Akatsuki, claimed he would make them pay, but Jiraiya gave him a harsh reality check as they stared down at what remained of Sasuke after the battle. Gai took Sasuke back to the village, but offered Naruto a gift – a jumpsuit like the one he and Lee wore. Jiraiya, once Gai was out of earshot, told Naruto he would forbid him to wear it. Being serious, he then told Naruto what it was they wanted – the Kyuubi inside him, to use it for their own ends. Naruto simply decided that he’ll become stronger to defend himself from them and continued to ask about Tsunade. Jiraiya told him that during the search, he’ll be concentrating more on Naruto’s training. Naruto popped the jumpsuit out again, but Jiraiya refuses to allow him to wear it.
While in the next town over, the place where Tsunade was rumored to be, Jiraiya also taught Naruto a lesson in vices – that money, women and alcohol are detrimental to the ninja way. And to stop Naruto from becoming greedy, he confiscated his bulging wallet and gave him a smaller amount, plus his luggage including the toad-summoning scroll in case they lose each other. Later, Naruto found Jiraiya sitting in a fancy bar, accompanied by a pair of girls, drunk and with Naruto’s empty wallet on the table. During the following scuffle, Naruto stains the jacket of a passer-by: a former Hidden Rock ninja, who tried to extort the money from Naruto or else. With lightning-fast reflexes, Jiraiya unleashed a swirling maelstrom of chakra from his hand and sent the attacker spiraling away into a water balloon stand.
As Naruto and Jiraiya left, Jiraiya bought the remainder of the water balloons and gave them to Naruto, telling him that the move he just used will require extremely difficult chakra control. Over the next few days, Jiraiya slowly gave Naruto more hints on how to successfully perform the move, allowing Naruto more time to work on it while he collected information on Tsunade and revealing the origin of it – the Fourth Hokage invented it, took 3 years to finally complete it and broke down the training for it into numerous steps. The complexity of it earned it a spot among the highest ranked techniques. Bit by bit, Jiraiya helped Naruto to learn it, also marking his hand as a focal point.
Eventually, Jiraiya traced Tsunade to the direction of Tanzaku Castle. However, he arrived to find it in ruins and reports of a giant snake. Later, Jiraiya finally bumped into her in a pub and spits out his purpose, shocking everyone including Naruto with the request for her to be the Fifth Hokage. Tsunade declined firmly, but Jiraiya later tried to talk her into it over a drink, also deducing the snake was present because of Orochimaru and that if she undid what the Third Hokage did to protect his village, she’d be an ally to Orochimaru and an enemy to him.
A week passed and Jiraiya tried one more time to convince Tsunade to accept the position over a drink. However, Jiraiya fell foul of her when she spiked his drink, waking up on the day that Tsunade planned to meet with Orochimaru with a stinging sensation all over, barely able to hold chopsticks let alone stand or use any moves. Tsunade had already gone ahead and turned on Orochimaru by the time Jiraiya caught up with them, bringing Shizune, Naruto and Ton-Ton with him. Naruto was surprised to see Kabuto alongside Orochimaru, where Jiraiya pointed out Kabuto’s allegiance was on his forehead protector, now bearing the Hidden Sound logo. Jiraiya then told Shizune to keep an eye on Kabuto as he went after Orochimaru directly. The two were equally matched, fighting atop the incapacitated serpents that Orochimaru had summoned that were stuck in a gigantic artificial swamp Jiraiya made, even though he complained that it wasn’t his usual level of capability.
It wasn’t until Orochimaru noticed Naruto’s use of the Rasengan that Jiraiya slipped up, having fended off Orochimaru’s direct attacks with his unusual body by turning his hair into spiny projections. As Orochimaru hurtled towards Naruto, Jiraiya was caught in a sucker-punch, still groggy from the drug and ending up being ensnared by Orochimaru’s tongue, sent to the ground with immense force. Still working it from his system, he finally got back up as Tsunade escalated the fight by bringing her summoned creature, the slug Katsuyu, forcing Jiraiya to back her up by calling on Gamabunta’s help. Gamabunta, as usual, was shocked to see the other major summoned creatures and joked at a reunion. Jiraiya set him straight that it was a battle against Orochimaru.
It was in this battle that Gamabunta showed another example of his flexibility and co-operation as he and Jiraiya simultaneously fired a stream of oil and flame respectively, resulting in a massive inferno that engulfed Manda, Orochimaru’s massive anaconda. However, Jiraiya noticed that Manda had escaped and shed his skin, cleverly hiding underground. As Manda popped out, Gamabunta and Jiraiya attacked it, only to find it was a fake-out as only the tail emerged. Manda’s fanged jaws opened up behind them, but Tsunade drove Gamabunta’s tremendous dagger into Manda’s head, pinning the jaws shut. The entire ordeal left Jiraiya with a broken rib and leg.
Jiraiya was also responsible for easing Tsunade back into Konoha, showing her to those who needed her medical skills. It wasn’t until the fight between Naruto and Sasuke on the roof of the hospital that Jiraiya reappeared, where he and Kakashi scolded each other for teaching the boys such dangerous techniques as Rasengan and Chidori, despite the necessity. Kakashi also hit a sensitive spot with Jiraiya, pointing out their rivalry wasn’t too far from the one with him and Orochimaru.
A short time later, Jiraiya realized the full gravity of the situation as Naruto returned, being carried by Kakashi after failing to apprehend the rogue Sasuke during his betrayal and defection to Orochimaru. Visiting Naruto’s hospital bed, he assured Naruto that the two were now officially teacher and apprentice for three years, due to his research on Akatsuki and Orochimaru revealing that Orochimaru wouldn’t be able to take over Sasuke until that time had passed. Despite the good news, Jiraiya also brought bad and told Naruto to forget about Sasuke, drawing on his own personal experiences and recalling his own attempt to stop Orochimaru leaving. The two parted on good terms, agreeing that the training will begin officially for Naruto in several months time.
Before their official training began, Jiraiya gave into Naruto’s whim to find Sasuke; perhaps recognizing his own desires to redeem a colleague, leading Naruto and Sakura on a brief but ultimately failed mission into the outskirts of Orochimaru’s lair. While helping a clan that Orochimaru used and abused, Jiraiya’s weakness for women was exploited multiple times, even with a custom-made trap set just for him when one of the Fuuma clan’s members was hypnotized, dressed as a geisha and made to seduce Jiraiya, then attack. The so-called “Koto Princess” clearly wasn’t enough to stop him and Jiraiya rescued his Genin charges, bringing them and two of the Fuuma members back to their clan. Needless to say, the incident put both Naruto and Jiraiya off venturing back there without further information.
Soon enough the time came and Naruto and Jiraiya left Konoha behind and officially started on their training journey. During the time that passed, Jiraiya continued his novel series as well as his research into Akatsuki, Orochimaru and now with Naruto by his side, the Kyuubi. Concerned for Naruto’s phenomenon of Kyuubi manifestation, where the Kyuubi appeared around Naruto as a fox-shaped aura of bubbling red chakra, Jiraiya developed a patch that would neutralize it when placed on Naruto. Unfortunately this was not before Naruto went into a four-tailed fox aura form. This deadly berserk Naruto managed to strike Jiraiya causing a large scar to develop on his chest. Not much else is currently known about the training, other than Naruto was able to improve on his Rasengan and endured exercises so tough, most of his clothing was worn through, even requiring him to move the metal plate on his forehead protector onto a new, bandana-like piece of fabric.
After three years, Naruto and Jiraiya finally returned to the village. Jiraiya returned Naruto to Kakashi's care and as a precaution, he supplied the suppression patch to Kakashi in case Naruto ran wild. He also reminded Naruto that there was a technique in his arsenal he should not use. After Kakashi and the team returned to Konoha from saving Gaara, Jiraiya met with Tsunade and Yamato in Kakashi's hospital room as he recuperated. With Kakashi out of commission due to his usage of the Mangekyou Sharingan, Naruto was turned over to the case of Yamato, the genetic heir to Shodai Hokage's bijuu controlling abilities. Jiraiya warned the group of the danger Naruto posed when he lost control to the fox aura, showing him the large scar he received from Naruto's four-tailed form.
A short time later Jiraiya and Tsunade met to discuss his plans to track down information on the Akatsuki leader. The two discussed their past history and Naruto's parents. He then made a promise that he would return and set off for the Rain Country. While there he captured two Rain missing-nins and inquired about their leader "Pain". Jiraiya then moved to summon Naruto's "Key", a sealing scroll which controlled the Kyuubi seal. Jiraiya asked that the scroll be given to Naruto in case he didn't return and then he set out again. Using one of the captured ninja, he managed to infiltrate the lair of Pain. He then soon learned that the two Akatsuki before him were his former students, Nagato and Konan. To Jiraiya's surprise he saw that though Nagato still bore the Rinnegan, he had a different appearance. Nagato would state that as "Pain", he was no longer a mere mortal, but a god.
As Jiraiya and Pain began to battle, Jiraiya was forced to call on the toad sages to assist in battle. Together they formed a new "Sennin" mode. This mode increased Jiraiya's power and gave him a more toad-like appearance. Together the trio managed to take out many of Pain's summoned animals. Pain responded by summoning two new ninja to his side, Akatsuki cloak wearing Rinnegan users. These new individuals used unique powers of their own and the Sennin soon determined that all three Rinnegan users were Pain, and shared the same vision between them. Jiraiya was forced to retreat and counter moved to distract all three of his opponents and eventually take them out one by one with the help of a paralyzing Genjutsu. With the job done, Jiraiya impaled all three men without full grasping what was going on. Jiraiya thus believed his prophecized choice to determine the fate of the world was finally made.
Out of nowhere Jiraiya was struck by another Rinnegan user. Jiraiya was launched through the city and had his left arm ripped off as a result. This new attacker then moved to revive his fallen comrades. Jiraiya then saw before him three more Rinnegan users, who were then joined by the three he had just killed. Jiraiya was then shocked to see one of the new Rinnegan users was an adult Yahiko, who Nagato claimed was dead. The six men known as Pain then moved to attack. Jiraiya retreated inside the stomach of a summoned toad. One Pain managed to infiltrate the toad barrier and stab Jiraiya with one of his strange black spikes. However, in the process he died. Jiraiya was then shocked to recognize his opponent. A man from the Fuuma clan he had fought years earlier, right after he began traveling the world to write his book. Determined to know the true nature of Pain, Jiraiya asked the Ma Sennin toad to return to Konoha with their defeated foe while he himself who leave the barrier to see if his theories were true.
Jiraiya saw this moment as his true prophecized choice, his decision here would have a great impact on the future of the world. Ma toad left, leaving Jiraiya and Pa Toad to investigate. Jiraiya emerged from the water and saw that the five remaining men before him were all ninja he had met in the past. In that moment he realized the true identity and nature of Pain. Before he could speak though, one Pain crushed his throat while the others impaled his back.
As darkness began to cloud Jiraiya's vision he thought back over his constant failures in life, how he couldn't save his student Namikaze Minato, the Fourth Hokage, his sensei Sarutobi, the Third Hokage or his friend Orochimaru. He thought over how he was constantly writing his partially auto-biographical book and his later embarrassment when he showed it to his student Minato. Minato stated he enjoyed the book and that the main protagonist, Naruto, was an excellent role model who reminded him of his sensei. Jiraiya was then honored to learn that Minato and his wife Kushina wanted to name their unborn son after the character. He also accepted their offer that he be the child's godfather. Jiraiya then thought over Naruto's drive and refusal to give up. And with that he made his mind not give up either. Jiraiya willed himself back to life to Pain's and Pa Toad's surprise.
Rising up he sent an unspoken message to Pa, who allowed Jiraiya to carve a numerical message into his back. Jiraiya realized Naruto was the actual child of destiny, and left his final message concerning Pain's true nature to him. Jiraiya left things in Naruto's hands and was then hit by another attack from Pain. Pa Toad fled and Jiraiya was launched into the murky depths finally content that he managed to do something honorable and worthy. With the book of his life complete, he would start his next tale, the Tale of Uzumaki Naruto. Jiraiya disappeared into the depths, having given his life for Naruto and the safety of his home village Konoha. Pain would later surmise that only by keeping his true nature a secret did he have a chance in defeating his former teacher. With Jiraiya passing on that knowledge, however, Pain's time may soon be coming to an end as well.