Instructions
Chapter 3, Episode 2: Guy vs. Guy
Get both Guys next to each other and do a basic B combo. When your Guy has full chakra and the other one doesn't, use your X attack. Finish him off with down A or forward A.
Chapter 3, Episode 5: Granny Chiyo vs. Sasori
Use down A a lot to hit Sasori wherever he is. A button combos have the best range, but you need to mix them up with B combos. If you need to get the puppets back to Chiyo quickly, use jump A or B. Even with these tips, it will probably take you at least 10 tries to beat this one.
Chapter 3, Episode 7: Naruto vs. Deidara
When you're close to Deidara, use down B to trip and start a combo. Jump B is a good combo starter from mid range. Down A is a good teleport attack for long range, but it can be dodged. Once you hit 75% chakra, use your jump X move, but Deidara must be in mid range in front of you for it to hit. Keep doing hit and run attacks until Deidara is down to 25% life and you have full chakra for your X attack. Keep in mind you only have 60 seconds to finish, so you don't have time to play defensively.
This episode is more of a puzzle than a fight. You control Guy and you have to beat a mirror image of yourself. When you attack, both Guys will do that attack at the same time. The only difference is your Guy has a slightly higher rate of chakra gain.
The key to this fight is being aggressive with the puppets while keeping them close enough to Chiyo for defense. Since you need to finish the fight with your jutsu, you probably only have enough chakra to do one substitution.
This is the hardest fight in the story mode. Deidara has super armor in the fight, which means attacks don't make him flinch, but he can still be tripped or knock down, and his explosives do extra damage. This will take quite a few tries to beat.