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When Link is navigating the hedge maze near the Palace of Darkness, a monkey named Kiki appears and follows Link. After exiting the maze, the monkey offers to follow him for ten Rupees. When the two arrive at the entrance to the Palace of Darkness, Kiki offers to open the door for a 100 Rupees. After Link pays this price, Kiki unlocks the door and goes away.
A monkey named Kiki aids Link in accessing Kanalet Castle; after being given some Bananas, the monkey calls its monkey brethren to help build a bridge. After the bridge is built, one of the monkeys will leave behind a Stick. There also exists a lone monkey on the Toronbo Shores that throws coconuts at Link.
Monkeys inhabit the Woodfall region of Termina. Link first encounters a monkey in the Woods of Mystery; the monkey guides him through the maze-like forest, leading him to an injured Koume. Upon Link's departure from the forest after aiding Koume, several monkeys appear before him, telling him of their brother who has been unjustly imprisoned for kidnapping the Deku Princess. After Link visits their brother in the Deku Palace, the monkeys provide him with information on how to sneak inside the monkey's cell.
Using a Magic Bean obtained from the Bean Seller as per the monkeys' instructions, Link is able to travel through the Inner Palace Garden to the monkey's cell. The monkey manages to explain the situation, as well as teach Link the "Sonata of Awakening", before his captors throw Link out, and begin torturing the monkey. Using the "Sonata of Awakening", Link is able to enter Woodfall Temple, defeat Odolwa and save the Deku Princess, vindicating the monkey.
Several monkeys appear in the Forest of Time along with many other types of animals. When Veran possesses Nayru and changes the flow of time, many of these monkeys disappear, as the disruption of the flow of time prevents them from ever being brought into existence. When Nayru is defeated, the restored monkeys are free to live in peace again.
Monkeys reside in Faron Woods, and are wrongfully considered nuisances by the villagers of Ordon Village. Early in the game, Link recovers a stolen cradle from a Female Monkey by using a Hawk. Talo, Malo and Beth later chase after a monkey. Link rescues both the imprisoned Talo and the Monkey. This Monkey later repays Link by using his Lantern to draw away the Poison Fog in the Faron Woods.
In the Forest Temple, Link finds and rescues several Monkeys, that help him cross broken bridges by hanging from ropes with their feet and using their hands to swing him across the chasms. The Monkeys eventually help Link reach the room containing the boss, Diababa, by forming a long monkey vine. Later in the game, a Monkey appears and tells Link of the location of the Sacred Grove.
The Light Spirit Faron resembles a monkey with a long tail.
Ook, the Baboon, is the leader of the Monkeys. This may mean that Baboons are considered part of the Monkey race, despite their striking differences, or that the leader of the monkeys is always a baboon because of this. Ook is the only Baboon in the Legend of Zelda series.
In Twilight Princess, monkeys aid Link inside the Forest Temple, which is implied to be their natural habitat. A female monkey guides Link on his journey to the Sacred Grove (much like Saria did in Ocarina of Time), suggesting the monkeys are actually transformed Kokiri, who, either by evolution or some other form of change, needed to better adapt to their changing environment. The monkeys also appear to have tattoos of the Kokiri symbol on their shoulders. The Forest Temple itself is theorized to be the remains of the Great Deku Tree from Ocarina of Time; this would also imply that Faron Woods, or some part of it, was once Kokiri Forest, which would also explain why the area is relatively uninhabited.
Hyrule Historia possibly debunks this theory, however, as it claims the only traces of the Kokiri left by the time of Twilight Princess was their symbol in the Forest Temple, implying they completely died out rather than evolving into a new form.