S-rank missions represent the highest level in the ninja mission system within Naruto. However, not all missions have their rank clearly confirmed by the manga. Some are explicitly labeled S-rank, while others lack specific classification despite their significant military or political impact.
3. Destroying Kannabi Bridge, A Mission That Changed the War’s Course
The mission to destroy Kannabi Bridge was a crucial campaign during the Third Great Ninja War. Minato Namikaze’s team was tasked with attacking the Stone Village’s supply line by demolishing Kannabi Bridge, a strategic location vital to the enemy’s advance.
Kakashi, Obito, and Rin took part in the operation, with Kakashi newly promoted to Jonin. Initially, Minato had another mission, so Kakashi was given command. However, the mission quickly became personal when Rin was captured by enemy ninja.
Kakashi insisted on prioritizing the mission, while Obito refused to abandon Rin. Their disagreement led Obito to return and rescue Rin, then save Kakashi after Kakashi’s eye was injured. Obito was then crushed by large boulders. Believing he was dying, he gave his Sharingan to Kakashi.
Ultimately, they succeeded in destroying the bridge and cutting off the enemy’s supply route.
The official Naruto site describes this as an attack on the Stone Village’s supply line and confirms the team completed the mission, though it came at the cost of Obito’s sacrifice.
The manga does not specify the mission’s rank, so it cannot be confirmed as an S-rank mission. Still, given its critical role in the war and severe consequences, the destruction of Kannabi Bridge remains a strong candidate for third place.
2. Secret S-Rank Mission, Protecting Two Jinchuriki
The secret S-rank mission is one of the few missions in Naruto explicitly confirmed as S-rank. As the Fourth Great Ninja War approached, the Allied Shinobi Forces had to hide the whereabouts of Naruto and Killer B. If Akatsuki discovered their location, both would become prime targets.
To keep their positions secret, Aoba assigned Naruto an S-rank mission. However, to prevent Naruto from learning the true purpose, he was given a completely different task. Naruto believed he was sent to the island to study local wildlife, while Leaf and Cloud ninja secretly protected him and Killer B.
What seemed like a humorous situation quickly turned serious when Kabuto and Deidara were resurrected and attempted to capture the two Jinchuriki.
The mission’s true importance became clear: Naruto and Killer B were the enemy’s most valuable targets. If captured, Akatsuki would gain access to the remaining Tailed Beasts’ power, advancing their larger plans.
1. Uchiha Clan Massacre, A Secret That Changed the Leaf Village
The Uchiha Clan Massacre is easily one of the darkest missions ever carried out by a Leaf Village ninja.
After discovering the Uchiha clan was planning a coup against the Leaf Village, Itachi faced an impossible choice between loyalty to the village and love for his family. Danzo gave him an ultimatum: allow the coup and risk civil war, or eliminate the clan to protect his younger brother Sasuke.
Itachi chose the latter. He collaborated with Obito to slaughter nearly the entire Uchiha clan. Sasuke was deliberately spared, while Itachi became a rogue ninja taking full responsibility for the tragedy.
This was not just an assassination mission. It involved secretly wiping out an entire clan within the Leaf Village, hiding the truth from everyone, and preventing a larger conflict.
Itachi’s mission records note he completed an S-rank mission, though the official storyline never explicitly confirms it was the Uchiha massacre. Still, it remains the strongest candidate for that S-rank mission given its extreme secrecy and consequences that affected the entire village.
The scale, secrecy, and risk of civil war make the Uchiha Clan Massacre the most dangerous mission among the three discussed here.