Madara looks down at Nagato and sucks him in. Nagato's corpse falls into Madara. All that is left now is Yahiko's corpse.
Konan's corpse floats up in the lake. The origami that is stained with blood from her chest catches the wind and takes flight.
Flashback.
Jiraiya and the three of them in the small hut. In the hut, there is a red board on the wall. Jiraiya says "From the right, these are Konan, Yahiko, and Nagato's."
"What's that" the three ask, "frog boards" he replies, the board is red on the front and white on the back, and on the white side there is a picture of a frog.
Jiraiya explains with a grin that if you turn it over, there's a frog.
When they are in the hideout, they are to leave the board on the red side, an when they leave the hideout, they should turn it over to the white side.
Jiraiya explains with another grin that the frog drawn on the white side is a frog signal.
Yahiko: "Just cuz you're the frog sennin so we're overlooking it, but you're pushing the frog onto us."
Konan: "Why do we have to do all that?"
Jiraiya: "This place still doesn't have public order, so we don't know when we'll get targeted. You're the easiest target when in the hideout, and if your location is leaked then a secret attack is also easy to launch"
Konan then understands from listening to him "Even though the board stays red, if that person is not inside the hideout, it means that he's been abducted by the enemy or something. If it's white but he's been inside all along, it could mean that there is a possibility that the enemy has transformed into him.
Jiraiya says that it'll be a code just for the 4 of them to confirm each others presence and they cannot let their guard down even in the hideout.
He has also built an underground hidden room, and he shows them the way to get out to the surface from it. He shows them his board, saying that it is the one behind them.
Jiraiya asks if they shall go do some "water off a duck's back" training. Yahiko runs out of the door.
Nagato: This time sensei has done it for us, but does he really get the stuff about this code?
Yahiko looks back: I'm gonna get even stronger and change this country (*pun. kaeru = frog = change)
Konan's cheeks flush a little. Nagato notices, "...." and then smiles
Jiraiya gets angry at Nagato: Before changing (kaeru) the country out there, first turn over the frog (kaeru) board!
Jiraiya then leaves the three. Jiraiya's board in the hut is on the frog side.
The three of them continue their training. When Nagato is out, Konan takes care of Yahiko. Their eyes meet and they stare at each other...
Nagato is pleasantly standing at the entrance with his back facing them.
Yahiko: Our organisation has grown large, today we say goodbye to this hideout. Everything began from here. For the sake of the realisation of our dreams, we will also depart from here! And...
There are 2 shinobi outside the hut. Before leaving the hideout, they turn the boards to the frog side.
However, as Konan's board is changed to the "out" side, a kunai with explosive tags on it hits the roof and explodes. A hole opens up in the roof.
Nagato as he escapes (via the path Jiraiya taught them from the hidden room): The hidden room served us well in the end
Yahiko: Let's go
End of flashback.
The origami that took flight from Konan's chest flutters towards the hideout of their beginnings that stands on the side of the lake.
The hideout has fallen into disuse and there are now trees and moss growing on it, but the frog boards, with moss growing on them are still as they were before.
Continuing from where Yahiko had said "And..."
"And... When our dreams come true, even if we're separated from each other... Let's return here one day. And then the three of us'll congratulate each other!
After those words, the red origami flies to Konan's frog board that had been turned to the "out" side...
Light shines in through the roof and through it a rainbow can be seen, as if a depiction of congratulations.
"Then at that time, we've gotta invite Jiraiya-sensei as well" "Yeah..." "Well... I wonder if that'll happen..." a conversation of the three from the past.
Jiraiya's board that had been turned to the "out" side when they parted ways has been flipped to the red side because of the trees that had grown and pushed it.
Madara and the rest. Madara puts on a new mask. "It caused some trouble but you managed to get some good eyes, didn't you" says Kabuto. Madara: "They were mine to begin with."
The information from Kisame has arrived as well, Zetsu holds out a scroll and says that things are in their favour.
Madara: "I'm off to get the Kyuubi" Madara stands, a weird weapon-like thing (a fan that is shaped like a gourd and appeared in Journey to the West or something?) in his hand.