- One sidequest involves Might Guy, Bee and Neji. Bee and Guy trains at rap while Neji does the Only Sane Man and ask help from Naruto who joins Bee and Guy. Neji does not join the party until Bee and Naruto says Neji is unable to do rap and since he is too proud and serious, he won't do it. Neji is quite insulted and joins the party and starts to rap with Bee, Naruto and Guy. Hilarity Ensues.
- Naruto comments "Even Neji does crazy stuff, he's in Team Guy all right."
- The kicker was the narrator: "By the time Neji realized the rapping was no use to his training, three hours had already passed."
- Guy getting seasick on your arrival at Turtle Island. Even when nauseous he chews the scenery. Then if you speak to Aoba, he comments this is the first time he's seen Guy like this...and really wishes he could get a picture of it.
- Mood Whiplash example: just as Naruto is getting ready to fight the Nine Tails in a Battle in the Center of the Mind...Killer Bee's giant hand pops out of the ground. He then offers to assist you in the fight...like that.
- The post-story mission in which Naruto faces an "Ultimate Decision" about what kind of girl he prefers: girls like Hinata or girls like Sakura and Ino.
- Another post-game Ultimate Decision involves choosing how to go about curing the Tsuchikage's back pain. The Hero path reduces it to a Fetch Quest, while the Legend path has you use "shock therapy"... i.e. actually fighting him. What's even funnier is that, if you go this way, you get a Don't Try This at Home disclaimer about how you should never try this on someone who has actual back pain in real life, and it's styled in the same way as the game's tutorial messages!
- The best part? It actually works, to the surprise of everyone except Naruto, of course.
- Naruto calls Mei (the age-conscious Fifth Mizukage) Née-chan and she gives him candy.
- At the end of her Post-Story quest, out of all the men in Konoha she scouted as potential future husbands (her actual motive for touring the village with Naruto), she chooses Naruto and decides to return when he's older. Also counts as Heartwarming, considering it's proof of how much Naruto has matured from the young ninja kid in Chapter 1.
- The sidequest that involves Kankuro, Ao and Akatsuchi needing a special medicine from Shikaku. After a Fetch Quest to find a Microshroom, Naruto can either take the Hero path and choose who gets the medicine...or choose the Legend path which involves Naruto threatening to eat the shroom himself to stop the trio from fighting...which culminates in them fighting Naruto to stop him from sending the shroom "down the haaaaatch!". Just seeing a trio of Kage-bodyguards getting so desperate when Naruto is about to down the thing is hilarious in itself!
- Bee shipping Naruto and Hinata. Hinata's Adorkable reaction is the icing on the cake.
Funny / Naruto Shippuden: Ultimate Ninja Storm 3
For all the awesome and epic moments in the game, Storm 3 does make us laugh quite a bit.