After his experience falling into the cave and finding his inspiration of fear inducing justice, the blonde and the pineapple hair Boys trained nonstop. Together they used all the known jutsu, learned from their senseis and passed them on to eachother, adding to their arsenal and even made their own jutsu like Narutos new shadow bat swarm, learning from Shikamarus knowledge on the naras clan, Naruto found how to mold the shadows into projections that when mixed with wind chakra, caused a painful distraction.
Shikamaru made a jutsu based on the fourth hokages famous rasengan, completing a shadow hidden swirl of death. The two Boys also trained with various samurai and retired shinobi becoming close to high jonin level. Their taijutsu is better then any hand to hand combatist even to say, can dispell chunin level shinobi from completing a jutsu and can maybe survive a encounter with a kage.
The jutsus they knew from konoha were increased tenfold after Naruto found a way to make a blood clone, sending many to villages henged so they became shinobi.
Many became Anbu, jonins and learned all secrets In their respective village, due to the trust their kages have in them from how loyal Narutos clones were. Then after learning everything from fighting styles, jutsu, craftsmanship, etc they would go [MIA] and poof relaying all the information to a meditating blonde. Naruto gaining the info would smirk and gather his lazy friend to Shikamarus disappointment.
Shikamaru after gaining far more control on his chakra sent henged shadow clones to get jobs, gaining a very hefty currency that was spent on various electronics and filing papers to write down evidence and information on their enemies. Naruto began studying human philosophy and psychology. Catching on very quick how to be observant with people, then read a thorough read being a detective, learned chemistry on poisons and antibodies. Naruto made his own weapons being a tad obsessed with bats made them bat related.
Bat shaped shurikens, bat smoke bombs, explosive bat tags, a hefty bat shaped kunai with bat like wing prongs, Etc etc
His greatest accomplishment however is his new ninja suit ofc bat related, after taking his time thinking on a light weight suit filled to the brim with scrolls of fuinjutsu (oh yeah Naruto learned his Uzumaki heritage so he is a master of seals) and all his other gadgets he came up with a anbu like appearance with a black cloak with jagged ends, his mask is smoky grey pointed ears and a bat like face that covers his whole face and head protecting him from blows to the skull.
Naruto also had retractable gauntlets that can fire knockout poisons and even lethal ones, he is clad in a anbu like vest with mesh armor underneath, grey shinobi pants and black ninja shoes with metal edges making kicks from naruto almost a knockout.
Shikamaru stays in the base they made in the cave, due to him not wanting to deal with violence anymore and as the lazy Nara he is. He stays and helps by communicating with Naruto through radio ways helping him with advice and troublesome predicaments, Narutos missions of assassinations, infiltration and information gathering. When done the blonde sends a bat with a report so shika can look over it and divulge in plan making. Naruto is usually out traveling, sneaking finding out all he can taking out missing nins and threats to whatever civilian he meets.
Shikamaru is now 15 as is Naruto. Together they help one another stay sane by Naruto getting supplies whilst on missions and sending them via "Bat travel" and shika the Medic after learning all he can with Medical ninjustu Shika heals Naruto or "Bat" as his codename and technically his is "shadow" things have been going well for them they, still are creating plans on how to save Konoha just getting stronger for that time.