After reading the comments and seen that some people were upset about the fight and how it doesnt make sense at all, let me break it down.
1) Konan and ALL of the six paths of pain had been buffed up so they are not like their anime counterparts
2) I'm not going to lie, I should have never made Y/n run out of chakra as someone did say he is an Uzumaki and a jinchiriki which is true but it just worked for plot convenience
3) This fight was also to humble Y/n a little and to take him out the picture so people like Naruto and Sakura can shine since they haven't been seen much
I hope this clears everything up.
It starts with Naruto and Kakashi walking towards the Hokage's office as they both enter to see Tsunade, Shizune, Sai, Sakura and even Fugasaku there.
Naruto: Huh? What is going on?
Everyone has sad faces on as they were looking at Naruto
Fugasaku: So he is Jiraiya-boy's student and the twin of Y/n-boy?
Tsunade: Yes...this is Naruto Uzumaki. The "Child of Prophecy" That you mentioned.
Naruto: Why is a geezer frog here? What does he want
Tsunade: Oi! Watch your mouth, Naruto! This is Lord Fugasaku one of the great sages at mount myoboku.
Naruto: So! What does he want with me?
Tsunade: He is here to speak to you.
Fugasaku: You are, without doubt, Jiraiya-boy's student and your attitude is a bit like Y/n's!
Naruto: Jiraiya-boy!? You talk as though Pervy sage is a little kid! Who do you think you are!
Tsunade: What did I say!? I said to watch your mouth Naruto!
Shizune: He is the man who taught Jiraiya sage jutsu. He is his master
Fugasaku starts to laugh
Fugasaku: Pervy Sage huh? What a fitting name for Jiraiya-boy!
Naruto: So what do you want with me then?
Fugasaku: I don't know where to start....where should I begin...
Fugasaku thinks for a moment
Fugasaku: The most important thing is.....Y/n-boy is gravely injured and probably dead
Naruto looks at Fugasaku with a straight face
Naruto: Eh?
Naruto: W-what are you talking about?
Everyone's faces were that of very sad looks as Sakura was almost on the verge of tears as well as Tsunade and Shizune
Fugasaku: I know this is sudden...
Fugasaku sighs
Fugasaku: For some time, it was rumoured that the leader of the Akatsuki was in the hidden rain village. So Jiraiya-boy personally asked Y/n-boy to come with him on the mission with him to which Y/n-boy agreed to.
Sakura: The leader of the Akatsuki was in the hidden rain?
Sai: It is a hard place to get into
Kakashi nods
Kakashi: But they were still able to get in
Fugasaku: There, Y/n-boy and Jiraiya-boy come up against the leader Pain.
Fugasaku: Pain was a former student of Jiraiya-boy.
Sakura: Student!? Jiraiya-sensei had students?
Tsaunde explains to them about Nagato, Konan and Yahiko
Tsunade: I didn't expect them to turn out like that...
Kakashi: But to corner the likes of Y/n and Lord Jiraiya..? How did Pain do it?
Fugasaku: He possessed the rinnegan just like Y/n-boy!
Kakashi was shocked
Sakura: The rinnegan?
Shizune explains the rinnegan to Sakura and how it's a jutsu that was with the sage of six paths
Fugasaku: And not only that...there were six of them who had the rinnegan also!
Kakashi: No way! How is that possible!?
Fugasaku: We learnt the trick of Pain but Jiraiya-boy is currently looking after Y/n so he can't tell us right now
Fugasaku looks down to the ground
Fugasaku: Y/n-boy decided to go up against the main Pain alone...we were not able to know what in the world happened to him till we saw him floating on the river
Sakura and Tsunade looks down to the ground...
Fugasaku: We tried to escape! But Y/n got hit with blasts and paper from the blue haired girl. And that then led us to now...
Fugasaku looks at Naruto
Fugasaku: I have now told you everything...
Naruto was looking down at the ground tears about to swell in his eyes
Naruto: You let them go didn't you granny..?
Tsunade looks at Naruto with a weary face
Tsunade: That's right
Naruto: Why would you allow such a reckless thing!? You let my brother and Pervy Sage go into a reckless place like that!? How dare you.!!!!
Naruto started screaming but Kakashi holds him back
Kakashi: Enough Naruto! You of all people should know how Lady Hokage is feeling...
Naruto looks at Tsunade as she looks absolutely depressed with the fact she had almost lost Y/n and Jiraiya at the same time....she almost lost her loved ones
Naruto: Damn it!
Naruto turns around to the door and walks off
Sakura: Naruto!? Where are you going!
Naruto looks towards the door
Naruto: If Pervy sage was the fifth Hokage instead of Granny..he wouldn't have let Granny take such a risk! Never!
Naruto opens the door and walks out. Sakura was about to go after him but Tsunade says her name
Tsunade: Sakura...it's alright. Just let him be.
Kakashi; I apologise lord Fugasaku...
Fugasaku: It's okay..I really believe that that boy loved Y/n-boy and Jiraiya-boy...
Naruto walked out of the Hokage's office as he starts to think of the times with him and Y/n and all the times that they were together and all the good times that they had
Naruto: I know that he may not be dead...I really hope that he isn't dead!!
Naruto continues to walk through the village with a depressed look as he feels wind past right past him as he looks up
Naruto: Y/n...
Naruto kept seeing things that reminded him of Y/n which causes him to smile. Naruto walks and sees Iruka
Iruka: Yo Naruto! I heard you were quite active on missions! Everyone in the village is talking about you! How about we go and catch up with some ramen?
Naruto looks down to the ground
Naruto: No thanks....
Naruto walks off leaving Iruka to wonder what happened to Naruto and what causes him to be like this.
Timeskip
Naruto was sitting on his bed as he looked to the other bed that was there but didn't see Y/n sitting there at all
Naruto: Why...
Naruto opens the door to his and Y/n's apartment as he walks towards a store that him and Y/n always used to steal from. He then sits down on a bench....
And just cries....
Iruka: Naruto...
Naruto wipes his tears as Iruka walks closer to him
Iruka: I heard what happened about Y/n....
Naruto stays there in silence
Naruto: I would have wanted him to watch over me...like he always did...I wanted him just maybe to see me become hokage
Iruka: He isn't fully dead Naruto...he still might have a chance
Naruto: But it's a small chance....and I don't know...
Iruka: I know Y/n wouldn't want you to be sad forever. He saw you as a brother he loved! He would never want you to be so depressed
Naruto: Thank you...Iruka-sensei...
Thanks for reading!!