It took me about half a year to put this timeline together; in order to do so I had to play sevral of the games, read walkthroughs and reviews, read about 15 Wikipedia articles, talk to people who've played the games I haven't and other various things. This is the Timeline for the Legend of Zelda games (minus a few really old ones that wouldn't fit) I hope you enjoy it!
The plot of The Minish Cap focuses on the backstory of Vaati and the Four Sword, which were important elements of Four Swords and Four Swords Adventures. The Picori, also called Minish, are a race of tiny creatures that bestowed a young boy with a green garment, a sword, and a shining golden light many years before the game is set. There are three types of Minish: Town, Forest, and Mountain.
The quests begins when Link is chosen by the king of Hyrule to seek the help of the Picori after Vaati had petrified Princess Zelda. Link was chosen because only children can see the Picori. On the voyage he rescues Ezlo, a strange being resembling a green cap with a bird-like head, who joins him and can make Link shrink to the size of the Minish. Although it is not revealed at first, he and Vaati were once Minish (Picori)—Ezlo a renowned sage and craftsman and Vaati his apprentice. Vaati became corrupted by the madness and hatred of men and took a magic hat Ezlo had made for the humans in Hyrule. The hat grants any wish made by the bearer, and Vaati wished to become a powerful sorcerer. He then turned his old master, who had tried to stop him, into a hat. With the help of Ezlo, Link retrieves the four elemental artifacts and uses them to restore the Picori Blade to the Four Sword, capable of defeating Vaati.
After Link restores the Four Sword, Vaati turns Hyrule Castle into Dark Hyrule Castle—the final dungeon in the game. Link fights Vaati just before he can drain Zelda of all her Light Force. Link defeats Vaati after engaging in a fight that consists of Vaati changing forms. When Link and Zelda flee from the collapsing castle, they meet Vaati as he again changes form for the final battle of the game. After the battle, Ezlo returns to his original form. He finds the cap of wishes he created and gives it to Zelda, granting her a wish. The cursed people are cured and the castle is turned back to normal. The hat overflows with the power of life and disappears. Ezlo gives Link a new hat and tells him that he enjoyed traveling with him, then leaves just as the Minish world closes
At the beginning of A Link to the Past, a young boy named Link is awakened by a telepathic message from Princess Zelda, who says that she is locked in the dungeon of Hyrule Castle. As the message closes, Link finds his uncle ready for battle, telling Link to remain in bed. After his uncle leaves, however, Link ignores his uncle's command and follows him to Hyrule Castle. When he arrives, he finds his uncle seriously wounded. Link's uncle tells Link to rescue Princess Zelda from her prison, giving him a sword and shield. After his uncle dies, Link navigates the castle and rescues Zelda from her cell, and the two escape into a secret passage through the sewers that leads to a sanctuary.
Link is told by a man in the sanctuary that Agahnim, a wizard who has usurped the throne, is planning to break a seal made hundreds of years ago by the Seven Sages. The seal was placed to imprison a dark wizard named Ganon in the Dark World, which was once the Sacred Realm before Ganon invaded, obtained the legendary Triforce and used its power to turn the realm into a land of darkness. Agahnim intends to break the seal by sending the descendants of the Seven Sages who made the seal into the Dark World. The only thing that can defeat him is the Master Sword, a sword forged to combat evil. To prove that he is worthy to wield it, Link needs three magic pendants. After retrieving the pendants, Link takes them to the resting place of the Master Sword. As Link draws the sword from its pedestal, Zelda telepathically calls him to the Sanctuary, informing him that soldiers of Hyrule Castle have arrived. Link arrives at the Sanctuary moments after the soldiers have vacated, where he learns from the dying man that Zelda has been taken to Hyrule Castle. Link goes to rescue her but arrives too late; Agahnim sends Zelda to the Dark World. Link then defeats Agahnim in battle but is subsequently also sent to the Dark World.
To save Hyrule, Link is required to rescue the seven descendants of the Seven Sages from dungeons scattered across the Dark World. Once the seven maidens are freed, they use their power to break the barrier around Ganon's Tower, where Link faces Agahnim again. After Link battles Agahnim for a second time, Ganon rises up from Agahnim's body, turns into a bat, and flies away. Link chases him, finally confronting him inside the Pyramid of Power in the Dark World. After a battle resulting in Ganon's demise, Link touches the Triforce and restores Hyrule to how it was before Ganon intervened.(he does'nt alter the past, he just restores Hyrule to the way it was.)
Link is tricked into thinking Zelda is in danger and draws the Four Sword, thinking that Vaati had escaped, and so splits into four and frees Vaati, AND on top of all that Links shadow is turned into his evil counterpart. After Link's mischievous alter ego Shadow Link begins wreaking havoc across the land of Hyrule, it's up to Link to use the power of the Four Sword to stop him. By using the Four Sword, Link can split himself into four Links, each a different color. After tracking down Shadow Link for the majority of the game, and defeating Vaati Link learns that Ganon was the mastermind of the sinister plot Link must then fight Ganon and beat him. Unbeknownst to Link he only drives him from the dark world and cures him of his beast form.
The events of Ocarina of Time take place before those of the first four games and are set in the fictional kingdom of Hyrule, the setting of most Zelda games. Hyrule Field serves as a central hub connected to several outlying areas with diverse topography. Some of these areas are populated by one of the races of Hyrule: Hylians, Gorons, Zoras, Kokiri and Gerudo.
The game opens as the fairy Navi awakens Link from a nightmare, in which Link is seen on a stormy night as a man on horseback chases Princess Zelda, who is being escorted also on horseback by a woman. Navi brings Link to the guardian of his village, the Great Deku Tree, who is cursed and near death. Link breaks the curse, but cannot stop the tree from withering. The Deku Tree tells Link a "wicked man of the desert" has cursed him and seeks to conquer the land of Hyrule and that Link must stop him. Before dying, the Great Deku Tree gives Link the spiritual stone of the forest, the Kokiri's Emerald, and sends him to Hyrule Castle to speak with the princess of destiny, Zelda.
At Hyrule Castle, Link meets Princess Zelda, who has been having dreams about the future of Hyrule and foresaw Link's arrival. She believes Ganondorf, the Gerudo King of Thieves, is seeking the Triforce, a holy relic in the Sacred Realm that gives its holder god-like power. Zelda's description of Ganondorf matches that of the man who killed the Great Deku Tree. Zelda asks Link to obtain the three Spiritual Stones, one of which he already possesses, so that he might enter the Sacred Realm and claim the Triforce before Ganondorf reaches it. Link goes to Goron City, where he meets Darunia, the leader of the Goron race. After Link kills King Dodongo, the boss of Dodongo's Cavern, Darunia gives him the Goron's Ruby, symbolizing brotherhood. Link next obtains the Zora's Sapphire from the Zora Princess, Ruto, after rescuing her from the belly of Lord Jabu-Jabu (a whale-like creature sacred to the Zoras).
Link returns to the castle, where Ganondorf is pursuing Zelda on horseback, as in his nightmare at the start of the game. Spotting Link, Zelda throws the Ocarina of Time into the castle moat and telepathically teaches Link the "Song of Time". After Ganondorf rides off, Link retrieves the Ocarina and uses the song together with the Spiritual Stones to open the door to the Sacred Realm. Through the door, Link finds the Master Sword, a legendary sword forged to fight evil. As he pulls the Master Sword from its pedestal, Ganondorf appears, having followed Link into the Sacred Realm, and claims the Triforce.
Seven years later, an older Link awakens in a distant room and is met by Rauru, the ancient Sage of Light and one of the seven sages who protect the location of the Triforce. Rauru informs Link that his spirit was sealed for seven years until he was old enough to wield the Master Sword and defeat Ganondorf. The seven sages can imprison Ganondorf in the Sacred Realm; however, five of the seven sages are unaware of their identities after Ganondorf transformed Hyrule into a land of darkness. Link returns to Hyrule and is met by the mysterious Sheik, who guides Link to rid five temples of Ganondorf's monsters, allowing the power of the temples to awaken the sages.
After awakening five sages, Sheik is revealed to be Princess Zelda and the Sage of Time. She tells Link that Ganondorf's heart is unbalanced, causing the Triforce to split into three pieces, as predicted in an ancient prophecy. Ganondorf kept the Triforce of Power, while the other two chosen by destiny carry the remaining pieces: Zelda gained the Triforce of Wisdom and Link obtained the Triforce of Courage. After Zelda bestows Link with the magical Light Arrows, Ganondorf traps Zelda in a magical crystal and takes her to his tower. The remaining six sages help Link enter the tower, where he battles and defeats Ganondorf, thereby freeing Zelda. After escaping the collapsing castle, Link is trapped in the castle area by a ring of fire and forced to battle Ganondorf once again; this time, using the power of the Triforce of Power, he transforms from his human form into a boar-like monster named Ganon. After fighting Ganon without his sword, Link eventually retrieves it, and, with the aid of Zelda's paralyzing light, delivers the final blow, which defeats Ganon. The seven sages trap Ganondorf in the Sacred Realm; still holding the Triforce of Power, Ganondorf vows to take revenge on their descendants. Zelda uses the Ocarina of Time to send Link to his original time to live his childhood. The game ends with Link and Zelda looking at each other in the castle garden.
Then the timeline splits in two (in both Ganon escapes the sacred realm rather soon.)
Timeline 1
Majora's Mask begins with Link riding his horse, Epona, through the Lost Woods after the events of Ocarina of Time. A masked Skull Kid and his fairy friends, Tatl and Tael, steal Epona and also steal the Ocarina of Time from Link and run to a dark cave. Link follows, and the Skull Kid turns him into a Deku Scrub. The Skull Kid runs away with Tael, abandoning Tatl; upset over the betrayal, Tatl agrees to help Link return to normal.
Link follows the Skull Kid through the cave to Clock Tower in Termina. He meets the Happy Mask Salesman, who says he can help Link if he retrieves the Ocarina of Time and Majora's Mask from the Skull Kid. They exit the Clock Tower in the center of Clock Town, which is preparing for the Carnival of Time. Link learns that the moon will crash into Termina in three days. He confronts the Skull Kid and Tael at midnight of the third day at the top of Clock Tower. He cannot take the mask, but he retrieves the Ocarina of Time and plays the Song of Time to send him back to when he first arrived in Termina.
The Happy Mask Salesman teaches Link the Song of Healing, which returns Link to his human form and leaves him with the Deku Mask. The Happy Mask Salesman tells Link that Majora's Mask grants its wielder's wishes, but possesses them with an evil, apocalyptic power. The ancient ones, fearing catastrophe, "sealed the Mask in shadow forever" to prevent its misuse. This tribe vanished and the origin and nature of the Mask was lost. The Skull Kid, possessed by Majora's Mask, is responsible for the moon threatening to destroy Termina.
Link travels between Woodfall, Snowhead, the Great Bay, and Ikana Canyon. Link enters a dungeon in each, defeating a boss that gives Link the power of one of the four giants that can save Termina. When all four have been completed, Link calls the giants, who halt the moon's passage towards Termina. Majora's Mask rises from the Skull Kid and enters the moon. With the help of Tatl, Link follows and defeats Majora's Mask. The Four Giants return to their sleep and Tatl and Tael reunite with the freed Skull Kid. The Happy Mask Salesman takes Majora's Mask, saying that the mask has been purified and its evil power has been destroyed. Link rides away on Epona as the Carnival of Time begins.
In this Timeline Ganon meanwhile had escaped rather soon and was executed by the sages. Afterward Link returns a century later to a world completely different. Also Ganondorf has been resurrected.
Twilight Princess takes place more than a century after the events of Ocarina of Time. When the story begins, Link lives in Ordon Village (a small town on the outskirts of Hyrule) and works as a ranch hand. A group of monsters suddenly attacks the village, kidnapping the village children and Link's close friend Ilia. Link pursues the attackers but unexpectedly finds the edge of the Twilight Realm. When Link approaches the Twilight, he is pulled inside, where the powers of Twilight transform him into a wolf, leaving him unconscious. A monster drags him off before he wakes up and imprisons him in Hyrule Castle. An imp-like creature named Midna appears before Link, helps Link escape his cell, and guides him to Princess Zelda, who is locked away in a tower.
A Shadow Beast pursues Wolf Link and Midna in the Twilight Realm.
In each of Hyrule's four provinces, Midna helps Link to collect Tears of Light, magical artifacts which restore power to the province's Light Spirit, who has the power to banish the Twilight from the area. In exchange for her help, Midna asks link to help her find three Fused Shadows, objects in which powerful magic has been sealed. Once Link finds two of the Fused Shadows, Midna explains that the Twilight King Zant is trying to change the Twilight Realm and Hyrule into a land of darkness using an evil power. Zant is a member of the Twili, a race of beings descended from magicians banished to the Twilight Realm by Hyrule's Light Spirits. Midna is also a Twili, but she is searching for the Fused Shadows to use their magic to defeat Zant and save the Twilight Realm. After restoring the four Light Spirits, Link and Midna reassemble the three Fused Shadows which were hidden inside three of Hyrule's dungeons, finding Ilia and the children along the way.
Zant then appears, takes the Fused Shadows, forces onto Link a crystal which traps him in his Wolf form, and critically injures Midna. Link rushes Midna to Princess Zelda, who reveals that the only way Link can become human again is to find the Master Sword. Zelda combines her heart with Midna's to heal Midna, allowing Midna to exist outside of the Twilight but causing Zelda to mysteriously disappear. After Link reaches the Master Sword, Zant's black crystal is forced out of him; Midna keeps the crystal, allowing Link to assume his wolf form at will.
Link and Midna travel across Gerudo Desert and climb the Arbiter's Grounds dungeon to reach the Mirror of Twilight—the only way to enter the Twilight Realm and stop Zant—only to discover that Ganondorf has broken it. The ancient sages who guard the mirror reveal that they banished Ganondorf to the Twilight Realm using the Mirror, and that he may be the source of Zant's newfound powers. They also state that Zant tried to destroy the Mirror completely, but could not because he is not the true ruler of the Twili. He was only able to break it into four fragments, of which three are missing. Traveling to the Snowpeak Ruins, the Temple of Time, and a City in the Sky, Link and Midna obtain the missing Mirror shards. After the Mirror has been restored, the sages reveal that Midna is the true ruler of the Twili–the Twilight Princess–and that Zant's curse turned her into an imp. When Link and Midna confront Zant in the Twilight Realm, he explains that he encountered Ganondorf while angry that he was not chosen as King of the Twili. Ganondorf offered to make Zant's wishes come true, and made Zant a vessel for his power. Midna regains the Fused Shadows and uses her ancestral magic to seriously injure Zant, stripping him of his power.
Link and Midna return to Hyrule Castle, which is surrounded by a seemingly impenetrable magical barrier, but Midna breaks through it with the Fused Shadows. They then encounter Ganondorf, who possesses Zelda, and Link is forced to fight Zelda. After Link defeats her, Midna purges Zelda of Ganondorf's spirit. Ganondorf then transforms into the form of a giant boar-like monster, Ganon. After Link defeats Ganon, Zelda's spirit is released from Midna's body, bringing Zelda back to life. Ganondorf then reappears in the form of a floating, flaming apparition that looks like his head (his "god" form). Midna teleports Link and Zelda to safety, and tries to destroy Ganondorf with the Fused Shadows. From Hyrule Field, Link and Zelda watch as Hyrule Castle is destroyed, suggesting Ganondorf has defeated Midna. Ganondorf appears on horseback holding the Fused Shadow that Midna once wore on her head. Zelda prays to the Light Spirits, who grant her the Light Arrows, and she and Link battle Ganondorf on horseback. Ganondorf falls from his horse in battle, and challenges Link to a sword-fight. After battling, Link drives the Master Sword into Ganondorf. Ganondorf stands, impaled, believing the Triforce of Power will save him. However, the image of the Triforce fades from his hand, leaving him to die. Because Zant's life had been tied to Ganondorf, Zant dies as well.
With Ganondorf defeated, the curse that Zant put on Midna is broken, and she regains her true human-like form. Link, Zelda, and Midna travel to the Mirror of Twilight, where Midna returns home. Before she leaves, Midna bids Link and Zelda farewell, and then cracks the Mirror of Twilight. Link is startled by this, realizing that he can never see Midna again. After Midna enters the portal the Mirror shatters, severing the only known link between Hyrule and the Twilight Realm forever.
Timeline 2
After the events of Ocarina of Time, Link travels abroad to train to combat further threats. After a storm destroys his boat at sea, he awakens on Koholint Island, and is taken to the house of a kind man named Tarin and his daughter Marin. Marin is fascinated by Link and the outside world across the sea, and tells Link wistfully that she would like to one day travel across the sea. After recovering his sword from Koholint's beaches, a mysterious owl tells Link that in order to return home, he must awaken the guardian of Koholint—the Wind Fish who is dreaming in a giant egg on top of Tal Tal Mountain and can only be woken by gathering and playing the eight instruments of the Sirens. Throughout Koholint Island, nightmare creatures attempt to obstruct Link's quest to awaken the Wind Fish as they wish to rule his dreamworld.
After collecting all eight instruments from the eight dungeons across Koholint, Link climbs to the top of the Tal Tal Mountain range and plays the Ballad of the Wind Fish with all eight instruments. This causes the egg where the Wind Fish sleeps to break open, and Link enters to face off against the Nightmare, who takes the form of Ganon and other enemies from Link's past. After Link successfully defeats the Nightmare, he plays the Ballad of the Wind Fish and both Link and the Wind Fish awaken; Koholint Island and all its inhabitants slowly disappear. Link finds himself lying on driftwood in the middle of the ocean, with the Wind Fish flying overhead.
Meanwhile Ganon escapes rather soon is captured by the sages then escapes and tries to take over Hyrule Link being on Koholint could not appear to repel the evil, and in response, the goddesses flooded Hyrule. The citizens were able to flee to the mountaintops, while Ganon and his army were trapped under the sea. The kingdom below was frozen in time to assure Ganon would not utilize his powers to escape, with the Master Sword as its key. The world above would be known as the Great Sea, and the memory of Hyrule was lost with time.
Set 100 years after the events of Ocarina of Time, The Wind Waker places the hero Link in a sea scattered with several islands, which necessitates frequent sailing and naval combat. Link lives with his grandmother and younger sister Aryll on Outset Island, one of the few inhabited islands of the Great Sea. The people of the Great Sea pass down a legend of a prosperous kingdom with a hidden golden power. Ganon found and stole this power, using it to spread darkness until a boy dressed in green sealed the evil with the Blade of Evil's Bane. The boy became known as the Hero of Time, and passed into legend. One day, the sealed evil began to return, but the Hero of Time did not reappear. The inhabitants of the Great Sea are unsure of the kingdom's fate, but it is clear that this legend is the story of Ocarina of Time.
When boys of Outset Island come of age, they are customarily dressed in green like the Hero of Time. The elders hope to instill the courage of the Hero in the children. It is Link's birthday as The Wind Waker opens, and he receives the familiar green tunic and hat. Aryll's present to Link is permission to use her telescope; as he looks through it, he spots a large bird carrying a girl to a nearby forest. After retrieving a sword, Link sets out to investigate. Link rescues the girl, only to have Aryll kidnapped by the same bird as it returns. The girl rescued in the forest is Tetra, captain of a pirate ship. At Link's request, they sail to the Forsaken Fortress, where a mysterious figure is holding Aryll and several other girls. Following an unsuccessful raid, Link is thrown from the fortress. A talking boat called the King of Red Lions rescues Link, and tells him that the master of the Forsaken Fortress is Ganon, the evil of legend.
The King of Red Lions gives Link the Wind Waker, a baton able to control the wind and move it in all directions, and instructs Link to sail the Great Sea in search of the three Goddesses' pearls. Link retrieves the pearls and takes them to the three Triangle Islands, causing the Tower of the Gods to rise from the sea. After battling Gohdan in the tower to prove his worth, Link sails into a ring of light and is taken beneath the waters to Hyrule Castle, overrun with enemies and frozen in time. Link descends a hidden staircase and finds the Master Sword, the evil-repelling blade used by the Hero of Time to seal Ganondorf. By removing the sword, Link awakens the castle and all enemies inside. He destroys the enemies and returns to the surface.
With the Master Sword in hand, Link returns to the Forsaken Fortress and joins Tetra and the pirates. He frees the captives and slays the Helmaroc King, but is easily overpowered by Ganondorf. Ganondorf tells Link that taking the Master Sword has fully lifted the seal, unbinding his full power; furthermore, the Master Sword has lost its own power to repel evil. Ganondorf lifts Tetra by the neck, and notices that she is wearing a fragment of the Triforce of Wisdom as a necklace. As he calls her Princess Zelda, two Rito that Link helped while finding the Goddesses' Pearls rescue Link and Tetra, and the dragon Valoo sets the entire fortress ablaze.
Link and Tetra sail back to the castle at the bottom of the sea and descend the staircase, where they meet Daphnes Nohansen Hyrule, the king of Hyrule and the voice of the King of Red Lions. He tells Link and Tetra that the prayers of the people in the legend were answered—the gods sealed Ganondorf and all of Hyrule with him by flooding the kingdom with a torrential rainstorm, ordering those chosen to take refuge on the mountaintops. The King combines a piece of the Triforce of Wisdom with the fragment in Tetra's necklace, causing her to transform into the traditional appearance of Princess Zelda. Link plays the Earth God's Lyric to Medli and the Wind God's Aria to Makar, awakening in them the knowledge that they are Sages of Earth and Wind. Their prayers restore the full power of the Master Sword.
Link goes on a variety of quests to find and decode eight Triforce charts that mark the locations of the pieces of the Triforce of Courage. Link raises the pieces from the sea and restores the Triforce of Courage, which dwells inside Link, marking him as the Hero of Winds.
With the restored Master Sword and the Triforce of Courage, Link returns once more to Hyrule Castle, where Zelda disappears before him. Link breaks through the barrier beyond Hyrule Castle and enters Ganon's Tower. Ganondorf reveals himself to Link, claiming that Link is the reborn Hero of Time and that fate has allowed him to bring the Triforce together again, just as he had with the Hero of Time. The three Triforces are extracted from Ganondorf, Link, and Zelda and combine to form the complete Triforce. As who ever touches the complete Triforce gets their wish granted, Ganondorf demands that the gods expose Hyrule to the sun once more, under his control. Before he can reach the Triforce, however, King Daphnes suddenly appears and touches the Triforce. He asks the gods of the Triforce to give Link and Zelda a future and to wash away Hyrule and Ganondorf. The Triforce splits apart and the ocean above begins to pour down all around the tower.
Knowing that the King has just ensured his own destruction, Ganondorf laughs and begins battling Link. Zelda assists by using Link's bow and shooting Ganondorf with Light Arrows. Once Ganondorf is stunned, Link plunges the Master Sword into Ganondorf's head, turning him to stone. Link and Zelda float to the surface in a bubble, leaving Ganondorf and the king to be buried underwater with Hyrule. Link and Zelda, now in the form of Tetra, sail away on the pirate ship and the now-lifeless King of Red Lions in search of a new land with the wind as their guide.
In the backstory to Phantom Hourglass's immediate precursor, The Wind Waker, a flood covered Hyrule, and only the tallest mountains, now islands, rose above the Great Sea. Phantom Hourglass depicts a different section of this sea than that of The Wind Waker, one which is the domain of the Ocean King. This section of the sea is split into four different quadrants, which can be explored after obtaining their corresponding sea charts. The final battle of Phantom Hourglass also takes place in a parallel world of The Wind Waker; this is confirmed after Bellum is defeated and the Ocean King tells them they must return to their own world. Set some time after The Wind Waker, Phantom Hourglass opens with Tetra and her pirate crew along with Link encountering a Ghost Ship claimed to have taken sailors and residents of the local islands in an area of the Great Sea. The crew discovers the ship, but when Tetra goes aboard to explore, she disappears; Link attempts to follow her but ends up adrift in the ocean.
Link later wakes up on a strange island through the help of the fairy Ciela (who has some amnesia about her past) and an old man named Oshus, who help Link on his quest to find the Ghost Ship and reunite with Tetra. To that end, they enlist the help of the reluctant Captain Linebeck and his ship after saving him from the Temple of the Ocean King; Linebeck only offers to help with the expectation of finding treasure along the way. Link discovers that to learn of the Ghost Ship's position, they must find the Spirits of Courage, Wisdom, and Power, using maps and clues hidden in the Temple of the Ocean King. However, to overcome the evil forces in the Temple, Link must make use of the Sands of Hours within the Phantom Hourglass and possessed by other creatures around the islands to prevent his life force from being drained.
With the aid of the Hourglass, Link is able to locate and ally with the Spirits of Wisdom and Power easily, but the Spirit of Courage he finds looks exactly like Ciela. Oshus explains that Ciela is actually the Spirit of Courage. Ciela is then reunited with the rest of her self, and awakens as the Spirit of Courage. With Link, they proceed to the Ghost Ship. He succeeds in his attempt to rescue Tetra with the help of the three Spirits, but finds that Tetra has been turned to stone. Link wants to find a way to save Tetra, but Linebeck refuses to help further, as there was no treasure. Oshus then reveals that he is the Ocean King, and that he and Ciela had to take their present forms to hide from the life-eating monster Bellum, who is the cause of the Ghost Ship, Tetra's statue form and other evil in the local area, and has taken residence at the very depths of the Temple. Linebeck quickly changes his mind as soon as Oshus promises to grant him one wish if he helps Link complete his quest to defeat Bellum and save Tetra.
Link learns that the only way to defeat Bellum is to forge the Phantom Sword from three unique, "pure" metals around the local islands called Crimsonine (found on Goron Island), Aquanine (found on the Isle of Ruins), and Azurine (found on the Isle of Frost). After collecting the materials and forging the Phantom Sword, Link descends to the bottom level of the Temple, and initially appears to defeat Bellum. Ciela's memory emerges during the battle which then helps to defeat Bellum. Tetra is freed from her statue form and revived, but before the group can celebrate, Bellum reemerges from the ocean depths and takes Tetra again. In the ensuing battle between the S.S. Linebeck and the Ghost Ship, Linebeck's ship is sunk with Oshus still on board, and Link and Tetra are captured. Linebeck reluctantly picks up the Phantom Sword and is able to free Link and Tetra at the cost of his own freedom, but is able to give Link back the Phantom Sword before becoming possessed by Bellum, turning him into a huge Phantom. Link is finally able to defeat Bellum without harming Linebeck.
As the adventure closes, the sand from the Phantom Hourglass is released into the sea. Oshus, now in his true form of a white blue whale, readies to depart with the Spirits of Power, Wisdom, and Courage, while Linebeck, surprising everyone, wishes not for treasure but for his ship back. After everyone says their goodbyes, Link and Tetra find themselves back on the pirate ship, where it seems only ten minutes have passed for the rest of the crew and they insist that the events were all just a dream. However, Link still possesses the now-empty Phantom Hourglass, and spies Linebeck's ship on the horizon (with the parts Link customized it with), knowing full well that his adventure was real.
Well, that's the best that I can piece the timeline together. However I'm not sure where Spirit Tracks fits in because I've never played the game or read the manga.