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...
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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
