Due to the fact that Y/n is kind of dead, he won't be in the Pain arc at all so this is going to be from the viewpoint of Naruto.

Naruto had went to the hospital as he went to where Y/n was being treated as he looks and sees Jiraiya standing next to Y/n who was in a hospital bed with strings all over him

Naruto: Jiraiya-sensei....

Jiraiya turns to see Naruto as he sighs

Jiraiya: Naruto....its good to see you

Naruto looks to see Y/n very very slowly breathing and one of his arms gone

Naruto: Why...why did Granny Tsunade send both of you on that mission!?

Jiraiya: We thought that we could come back just the way we went in...but everything powerful must come with a cost

They turn to look at Y/n's arm

Jiraiya: They took one of the Pain's to Autopsy, why don't you go and help them out there Naruto?

Naruto: Nah...I would rather stay with my brother...

Jiraiya smiles as he looks at Naruto

Naruto: At least....i didn't lose the both of you..

Jiraiya: And you won't lose Y/n either. Just have some faith Naruto...

Naruto: Thank you Jiraiya-sensei...

The door opens as Tsunade, Fugasaku, Shizune and Sakura walk in through the door

Sakura: Is that Y/n...

Yes guys, I decided to give the Seal to Sakura right now since I want her to surpass Tsunade in the very arc instead of the war arc

She gasps as she walks over to him and sees him laying there very still

Jiraiya: Is there something that you would like Tsunade?

Tsuande: It's not me that wants you...but Lord Fugasaku instead

Fugasaku looks to Naruto and Jiraiya

Fugasaku: Y/n-boy is down so we have lost firepower to strike back against Pain

Naruto: Wait Pain isn't fully dead yet!?

Jiraiya shakes his head

Jiraiya: I saw it...Y/n didn't do enough to take both Konan and Pain out...but they did a lot on him

Naruto: I'll avenge Y/n then! No matter how long it takes!

Fugasaku: Not to rude Naruto-boy...Y/n-boy is bounds ahead of you and you think at your current state you could be able to defeat Pain?

Naruto: So how can I do it!?

Fugasaku: This is mainly the reason why I came here in the first place. I was planning to come and get you

Jiraiya looks at Fugasaku

Jiraiya: You want to...

Fugasaku looks at Jiraiya and nods before looking back at Naruto

Fugasaku: Want to train in sage jutsu under my guidance?

Naruto: Sage Jutsu training? Is it that good?

Jiraiya: Of course it's good Y/n! I was the only one in the village who could use it

Tsunade: At this current point in time, since Y/n is down, No one in the village can beat Pain and Konan.

Fugasaku: I too want to avenge Y/n-boy after the effort that he put in! And I believe that you are the one who can do it Naruto-boy

Jiraiya nods

Fugasaku: If you want to avenge your brother follow me! I will teach you sage jutsu at Mount Myaboku!

Fugasaku: Everything I drove into Jiraiya-boy, I'll drive into you!

Jiraiya: I'll be coming also..you need all the training that you can get

Naruto: But who will be with Y/n...

Shikamaru: We will watch over Y/n...

The door opens as Shikamaru, Ino, Choji, Hinata, Shino, Kiba, Rock Lee, Neji and Tenten all walk in

Choji: You go get stronger Y/n!

Neji: We will take care of the person who changed our lives

Hinata blushes as she looks at Naruto

Hinata: W-we are rooting for you Naruto-kun

Ino: Go and make Y/n-kun proud!

Kiba: It's sad to see him like this...I really wanted to fight him again

Shino: He has the rinnegan Kiba, you would definitely lose:

Rock Lee: Fight with your hearts content Naruto!

Tenten: And we will be getting stronger here!

Sakura: That's right

Sakura puts her hand on Naruto

Sakura: So don't worry.

Everyone: We will protect Y/n.

Fugasaku: Sage jutsu training is more rigorous then you can ever imagine

Jiraiya: You will be up for it Naruto

Naruto looks off into the distance

Naruto: Let's do it! Just you wait Y/n!

Naruto, Jiraiya and Fugasaku walk towards the gate of the leaf village

Fugasaku: Now then, let us go. Naruto-boy say your goodbyes

Naruto looks to the Konoha 12

Naruto: I'm off! I'm counting on all of you to protect Y/n!

They all nod

Jiraiya: Oh! And one more thing just to let you guys know...the six paths of pain...aren't the real pain.

That leaves everyone in shock

Jiraiya: Oh well! See ya!

Naruto, Fugasaku and Jiraiya all reverse summon as they disappear in a puff of smoke. Naruto looks up to find himself in a different place

Naruto: Where are we...?

Jiraiya: The land of the toad Naruto.

Gamakichi: Naruto!!!

Gamakichi jumps down

Naruto: Huh!? Gamakichi?

Gamakichi: I summoned you here Naruto

Naruto: I see!

Fugasaku: Before we train, we must eat. Follow me

Jiraiya knows what's going to happen next as he signs

Naruto: Food!?

Naruto: What is this...

Shima: Eat up! Don't be shy!

Jiraiya and Naruto start to eat the food but Naruto feels like gagging

Jiraiya: You will get used to it Naruto.

They finish their food as they go to an area

Fugasaku: Now...it's time for you to start your training

Naruto: Yes Sir!

Fugasaku starts to explain to Naruto about Sage jutsu and how it works as Naruto doesn't understand what he is talking about so Jiraiya tries it but doesn't work.

Naruto: This makes no sense....

Gamakichi tries to explain it as Naruto understands it

Jiraiya: To be expected..it was easy enough to understand

Fugasaku: Let me show you what I am talking about.

Fugasaku picks up one of the tall rocks

Naruto: He lifted it!!

Thanks for reading!!