-SENJUTSU-
After Jiraiya's death at the hands of Pain, Naruto began training with Fukasaku in Myōbokuzan to learn senjutsu and how to enter Sage Mode. In order to achieve this, Naruto had to learn to sense and control the natural energy around him. Once mastered, Naruto was able to perfect the Rasenshuriken, so that he could throw it, and learn Frog Kata, the taijutsu style that uses the natural energy around the user to enhance the range and the potency of their attacks. However, Naruto had one fatal flaw in his senjutsu training. To mold senjutsu chakra, the user must remain absolutely still. Something one can not do while in combat, and because of the Nine-Tails, Shima and Fukasaku are unable to fuse with Naruto to mold it for him. To counter this, Naruto has to leave two shadow clones in a safe place to mold the senjutsu chakra for him. Once he depletes his current amount of senjutsu chakra, he would dispel one of the clones and gather it's senjutsu chakra to reenter Sage Mode.
-WIND RELEASE-
After failing to bring Sasuke back to Konoha, Naruto went through elemental training where he discovered that he had an affinity to wind, which by incorporating into the Rasengan, which was originally intended to be combined with a nature element, would greatly increase his power and his chances. The wind nature compliments a fighter like Naruto, as the wind nature is a good match with short ranged fighter. By focusing his wind chakra, Naruto can go as far as cut things with only his chakra. Naruto had learned nature transformations to upgrade his Rasengan, which he achieved with the Wind Release: Rasengan and the Rasenshuriken, combining both shape and nature manipulation originally deemed impossible without natural talent or instinct. The Rasenshuriken was capable of slicing into the victim and cutting them at a cellular level faster than a Sharingan can see it. It however caused similar damage to himself as it is still a handheld jutsu, despite it's name. After his sage training, he could throw the Rasenshuriken and expand it, increasing its power and attack radius.
-RASENGAN-
Created by the Fourth Hokage and taught to him by Jiraiya, the Rasengan is Naruto's second and strongest signature jutsu. While the Rasengan is a one handed technique, Naruto required the use of two to form it due to his poor chakra control, thus using a clone to form the "shell" of the sphere. Despite this, Naruto has used the Rasengan effectively in almost every one of his fights after mastering it. The Rasengan holds an advantage over its counterpart, the Chidori. The Rasengan only requires chakra control to form, while the Chidori uses so much chakra that it can only be used a few times a day. Naruto mastered the Rasengan to a degree that he can do it almost instantaneously. The Rasengan, like the Clone Technique, would be the base of several original jutsu created by Naruto, such as the Great Ball Rasengan, a larger version of the Rasengan, and after his wind training created the Wind Release: Rasengan and Wind Release: Rasenshuriken, and after his senjutsu training, the Sage Art: Great Ball Rasengan and Sage Technique: Rasenrengan. Due to the unique nature of the Rasengan in Naruto movies, Naruto creates a new type of Rasengan, often facilitated by a character in the movie, or a unique property present in the movie.
-TOAD SUMMON SKILLS-
Naruto was first taught how to use the Summoning Technique by Jiraiya. After allowing Naruto to sign the Summoning Contract with the toads of Myōbokuzan, Jiraiya took Naruto through the execution of the technique in order to provide Naruto with allies in future battles. Additionally, Jiraiya's other motivation to teaching Naruto how to summon, was in order to help Naruto to realize, and take advantage of, the Nine-Tails' chakra reserves. The type of toads that Naruto can summon at any time is proportional to his chakra and skill, as when he first started out he could only summon tadpoles. At first, Naruto would have a hard time getting any specific toad, as he would summon either Gamakichi or Gamatatsu. But when he used the Nine-Tails' chakra, or when he is truly motivated, Naruto was able to summon the toad boss, Gamabunta.
-SHADOW CLONE TECHNIQUE-
Naruto's first signature jutsu, the Shadow Clone Technique takes advantage of the massive chakra reserve Naruto possesses due to him being the jinchūriki of the Nine-Tails. Naruto is able to create upwards to two thousand clones, and able to have a decent amount of chakra in each of them. Because of this, Naruto can use his shadow clones for almost anything, from straight combat to training. In the beginning, Naruto would create a multitude of clones to overwhelm his opponents. Other times however, he would employ the use of the Transformation Technique to change the appearance of this clones to catch his target off guard. By Part II, Naruto learned that whatever his shadow clones learn, he, the main mind, will also learn. By using this, he is able to learn something that would take years in days. Naruto also learned that he could use the shadow clones to determine his opponents' abilities, to determine how many clones he will really need to defeat them instead of wasting chakra on thousands of clones.