This is a prediction I came up with a while ago.

Possesing the Rin'negan is probably an enormous gift but more of a burden. It's power, said to be a tool from the gods, most likely affected Nagato in a bad way, causing him to lose use of his physical body. Later on he killed Yahiko for some odd reason and Yahiko became the first Realm, the God Realm. The Realms are in full control of Nagato. Most likely Nagato was taken into Akatsuki and controlled into killing Yahiko. The same probably happened to Konan.

Now, Jiraiya mentioned in the Manga that all of the Realms were people he has encountered before in battle.

The God Realm was probably ordered to follow Jiraiya to take his body when he died. On the way he took the bodies of the people Jiraiya killed and "Pein-ified" them. After many years Nagato either saw that Jiraiya wouldn't die any time soon or needed the God Realm for something so he called it back to join the other Realms.

This would explain why all of the bodies were people Jiraiya killed before in combat.

He soon gained control of the Rain Village in search of more power.

I doubt his real goal is the one mentioned in the manga. That's probably just something to hide his true intentions.

Later on, Jiraiya met up with Pein and ended up getting killed while also putting up a great fight.

So if one of Nagato's goals was to obtain Jiraiya's body he now has it. The "Pein-ification" most likely takes a long time to occur and I personally think Jiraiya will end up replacing one of the Realms (maybe the one that just died in the manga) and Naruto will end up fighting him.

I honestly think this is what's going to happen even if you all may not like it that much. Again, this is just a short prediction. Reps would be appreciated. :p