15 years later...
Chouji: Chouji and Ino both return to their former lives as ninjas after seeing the destruction caused at the hands of sasuke and madara's attack on konoha.
Lee: Lee unfortunately dies during the second invasion of konoha while attempting to save sakura from being murdered at the hands of sasuke.
Naruto: Naruto and Hinata after a terrible fight with madara and sasuke have their connection to their bijuu permenently severed forcing them to have the bijuu sealed in naruto junior and their daughter, hiko. Naruto is told by sakura that if he ever fights madara again it could kill him so naruto puts all his focus on getting training for his children as he is told by the elder sage toad that they will have the power to defeat madara one day. Naruto is also concerned about jiraiya's friendship with Itachi as jiraiya has been missing for several months.
Neji: Neji returns to the ninja academy to serve as a defense trainer with the young students against the eventual war with akatsuki.
Sakura: Sakura continues her efforts to train hiko but is also seeks a way to repair the physical damage done to naruto at the hands of madara and sasuke. She is also greatly saddened at the death of lee and her failure to realize how great his love was for her.
Shikimaru: Shikimaru and neji prepares the older students for an eventual war that could take places as the ninja world prepares for what could be another ninja war against a newly revived akatsuki.
Tsunade: Tsunade trains the young hiko in the arts of advanced healing techniques as well as using them as a means of self defense. Hiko's access to the bijuu allows for much greater accuracy and control which convinces tsunade that if trained properly that hiko could be an even greater student than sakura was.
Kakashi: Kakashi convinces the other nations to hold a secret training event to train all the new jinchuriki in how to use the full power of their bijuu.
Guy: Guy joins kakashi in his endevor as he watches the last of his students successfully become chunin.
Garaa: Garaa prepares the sand village to assist the leaf village in its war against a newly revived akatsuki.
Itachi: Itachi helps jiraiya to break free of the brainwash so as not to repeat history with a massacre of the hyuga clan. Itachi convinces jiraiya that the key to defeating madara is to find a way to break edo tensei. Jiraiya agrees to undergo training with itachi in hopes of finding a way to grow as strong as his brother and sister.
Madara: Madara watches with curiousity as he watches the next generation stronger and stronger with each battle. Madara is angered that naruto was actually able to force him to retreat but is satisfied that naruto likely will never be able to fight again.
Sasuke: After his failure to kill naruto and hinata, Sasuke and Madara redouble their efforts to create a large enough ninja army to attack the ninja alliance.
20 years later:
Chouji: Unfortunately is murdered at the hands of Sasuke Uchiha as he attempts to defend Ino and senjuro as they defend the ninja academy children from a massacre at the hands of sasuke uchiha. Ino uses her powers along with senjuro to trap sasuke in a genjutsu believeing he is killing everyone at the academy.
Naruto: Naruto attempts another battle with sasuke after sasuke is forced out of the academy. Sasuke carries much of an advantage during the battle but naruto manages to knock him unconscious and prepares to deliver a killing blow when madara suddenly arrives to defend sasuke. Madara prepares to kill naruto when naruto junior arrives and vows that on this day he will destroy madara forever.
Neji: Neji with the help of shikimaru manages to save the lives of many civilians as they retreat below konoha to safety as sasuke and madara use powerful fire attacks causing a massive inferno throughout konoha.
Sakura: Sakura with the help of several other medic nins manages to stop sasuke's plague weapon before it can be spread throughout konoha. Without the plague, sasuke and madara are forced to attack the city itself head on instead of weakening it over time. Sakura helps shikimaru and neji send the villagers to safety as konoha is set ablaze by attacks from madara and sasuke.
Shikimaru: Shikimaru and neji decide that they are best suited at leading the survivors to safety rather than help in the battle. Shikimaru is unable to save chouji from sasuke but is able to distract sasuke enough that ino and senjuro are able to place a genjutsu on sasuke.
Tsunade: Tsunade passed away 1 year after the attack on konoha. It is believed by many she died of heartbreak as she saw the fragile peace that was created by the terrible war shatter due to her failure to realize how big a danger sasuke would become.
Kakashi: Kakashi after the war decides to take a new job as leader of anbu black ops after the death of ibiki at the hands of madara.
Guy: Guy takes an active role as a new teacher at the ninja academy teach the importance of tai-jutsu training as an alternative to ninjutsu and genjutsu.
Garaa: Garaa decides to make shikimaru's son the next kazekage as his years of abuse on his body from over using his powers during the war take a drastic toll on his frail body and mind.
Itachi: With the help of jiraiya, Itachi is able to find a way to cast edo tensei on kabuto thus raising him from the dead. Kabuto is at first skeptical of helping jiraiya but his main wish is to get revenge on sasuke so he agrees to end the edo tensei thus freeing his spirit as well as greatly weakening madara who is forced to rely on possessing sasuke uchiha in order to stay alive after naruto destroys what is left of his body.
Madara: As the edo tensei broke during the battle with naruto junior, Madara possessed the body of the nearby unconscious sasuke uchiha in hopes of defeating naruto junior however his plan failed as hiko arrived on the battlefield along with senjuro who manages to awaken sasuke within madara greatly disrupting madara's control of sasuke enough that madara is forced out thus causing his spirit to be released.
Sasuke: Sasuke after being possessed by madara is captured and imprisoned for the crimes he has committed. His son often visits him in prison but sasuke's only interest seems to be getting out in hopes of taking vengeance on naruto for all the losses he has endured.
Ahh time for a little q&a,
When did Sasuke fight Naruto after he defeated Tobi, since you mentioned sasuke failed to kill him or did you just skip that part?
That happened before the 1 year later mark. After that failure it slowly drove him to taking over the empire of orochimaru.
For those who can't figure out the pieces of this next one. There are 2 more attacks on konoha after the attack done by pain. The first invasion by sasuke and madara caused heavy damage including wounding or killing several individuals. The final invasion was the last straw in the war between the reborn akatsuki and the ninja alliance. In sense it was the final battle of madara and sasuke.