Naruto obtains all of turtles' weapons as opposed to just one of them.
Wave arc (ch. 6-10)
Chunin exam arc (ch. 11-20)
Almost all of it. Here are just some highlights:
The fights during the third part of the exam.
Neji getting beaten was one in-universe.
Hokage arc (ch. 21-24)
Naruto masters the rasengan, a skill that is known for being hard to learn and master.
When Manda is summoned, the turtles realize that Gamabunta and Katsuyu are in for a long fight. What do the turtles do? they go into their dragon mode-yes, the same one that the turtles used for Tengu Shredder-to fight alongside Bunta and Katsuyu
Rescue Sasuke arc (ch. 25-26)
New York arc (ch. 27-29)
Battle Nexus arc (ch. 30-33)
When Himeko enters her Isis form
Post Time Skip
Snow Country/Beach arc (ch. 34-40)
Everyone got far stronger in such time.
Itachi Returns (ch. 41-42)
Danzo arc (43-45)
Villain Alliance arc (ch. 46-48)
When Naruto and Sasuke combine their rasengan and chidori together to destroy Utrom Shredder's arm that was grabbing Himeko in his attempted Taking You with Me attempt