The answer, as with much manga source material, is dialogue and backstory -- though unlike, say, novels, you don't get the same depth and details that a book can offer. So to save you the trouble, I thought I'd summarize those additional details here (though if you're interested, you can always go to your local bookseller and pick up your own copy).
Note: The manga did take some artistic liberties with some plot points. I chose to include those that weren't blatant contradictions to the plot of the game. As you proceed, think of the points below as a summary of "deleted scenes."
Warning: Spoilers to follow.
- Link's mother, having fled a burning village, ultimately collapses in front of the Great Deku Tree, imploring him to take care of her newborn son.
- Gohma, in desperate search of the Kokiri Emerald, curses the Great Deku Tree, urging him to summon the young boy.
- The antagonistic Mido (armed with the Kokiri Sword and intent on earning Saria's affection) accompanies Link (with the Fairy Slingshot) in exploring the Great Deku Tree. After Link defeats Gohma, Mido offers the Kokiri Sword to Link (in addition to Saria giving the Fairy Ocarina) to aid him on his quest.
- In Castle Town, Link meets a young girl (not unlike Malon) who offers to show him the way to the princess if he plays with her for the day. They go around playing games, shopping, and exploring. At the end of the day, two Gerudo thieves attack the young girl. Link fends them off, but when they flee, he loses track of her. Disappointed, he follows her earlier directions and sneask into the castle courtyard. There he discovers the girl is none other than Princess Zelda.
- Before sending Link off, Zelda gives a blushing Link a kiss on the cheek. Navi begins teasing him about his ladies throughout his adventure.
- While loitering about Kakariko Village, Link rescues a baby dragon Volvagia, which learns to say his name.
- When Link finds Ruto, she reveals that she ran away because her father was arranging for her to marry another Zora. After rescuing her from Jabu Jabu's belly, Link laments about how his father figure (The Great Deku Tree) passed away. Touched, she offers her sapphire, and informs him that is now her fiancé (which Link doesn't understand).
- Once Link returns to a burning Hyrule castle, Impa flees will Zelda, who tosses the Ocarina of Time. Startled by a threatening Ganondorf, Link drops his Fairy Ocarina which Ganondorf recovers, mistaking it for the Ocarina of Time. Link proceeds to the Temple of Time, where he awakens seven years in the future.
- Later we see Ganondorf crushing the Fairy Ocarina, enraged for having been tricked by the young boy.
- Following the time skip, a defeated Stalfos spirit communicates to Ganondorf, revealing that the Hero of Time has shown himself.
- Deep within the Fire Temple, Link confronts Volvagia, his pet dragon from childhood. He hesitates to slay the dragon and Sheik steps in to save him. When Link regains consciousness, Sheik motivates him to confront Volvagia again. During the second fight, Link tries to get through to Volvagia to no avail. But when he slays the dragon, it softly utters his name before dying in front of a devastated Link.
- We then see Sheik kneeling in front of Ganondorf, revealing the details of the most recent battle. Sheik tells Ganondorf about Link's low spirits and advises that he should strike now. Ganondorf also inquires about Sheik's search for Zelda, reminding that Link and Zelda must not find each other.
- Link travels to Kakariko Village where Impa confronts him and subsequently scolds him for traveling so far without proper supplies. Link appeals to Impa so that she may train him to become a better fighter, and the two train for several days.
- While drinking from the Kakariko Village well, a black shadow materializes as Dark Link and challenges him to see how strong he's become.
- Following his battle and the completion of his training, Impa proudly pierces Link's ears and presents him with earrings as part of a coming-of-age ritual.
- In Ganon's Castle, Ingo apologizes to Ganondorf for losing Epona. As punishment, Twinrova brainwash the ranch worker, and Ganondorf commands him to go back and defeat the Hero of Time. He also tells Sheik, also present, to go with him and questions why a Sheikah would serve him and not the Royal Family as the tribe had in the past. Sheik simply reveals the tribe had no leader until Ganondorf came and leaves.
- Following the brawl with Ingo and Malon's rescue at Lon Lon Ranch, Link, resting on a rooftop, gets approached by Sheik, who instructs him to go to the Haunted Wasteland to search for Zelda. Sheik disappears before Gerudo show up. Link destroys the cursed jewel that keeps Ingo spellbound. After holding off the Gerudo for a bit with help from Malon (and her pitchfork), the two ride Epona and leap over the fence to escape the ranch.
- The Water Temple battle suggests that Ruto was acquainted with Morpha, the temple boss.
- Arriving disguised in Gerudo village, Link gathers supplies. At an open shop, a disguised Twinrova catch his attention and tell him to find his destiny at the Spirit Temple. After he leaves, Sheik arrives, who they tell to follow him. However, they question whether Sheik is secretly aiding the Hero of Time, which Sheik denies.
- Once Sheik departs, Twinrova summon Nabooru to help Sheik and determine if he is a traitor.
- During a sandstorm in the Haunted Wasteland, Sheik rescues Link and offers to guide him through the rest of the way to the temple. While traveling and setting up camp, the two have conversation which reveal several details.
- When Link inquires about the eye symbol on the outfit, Sheik reveals the eye was originally the symbol of the Sheikah, but they added the tear when the Royal Family betrayed them. Link asks if Sheik still bears a grudge, which Sheik denies. Link explains his story and discovery of being the Hero of Time. From his perspective, he just left Zelda, but he wonders how the years have changed her and feels uneasy to see her again. Sheik attempts to confort Link and dismisses it, saying it's hard to be a hero.
- Link has a nightmare about fighting off an army of Stalfos and upon waking up, Sheik reveals that in the Haunted Wasteland phantoms prey on travelers during the night. In the morning, a Gerudo party surround Link. Distracted, Link gets knocked out by Sheik and awakens unarmed in a Gerudo prison within the Gerudo Fortress.
- Following the fight with Nabooru, he flees from Gerudo guards and encounters Sheik blocking his path, holding his Master Sword and Hylian Shield. Throwing the weapons forth to Link, Sheik signals the desire to duel. As Link prepares to battle, Sheik instead turns on Twinrova behind him and then flees with Link. Twinrova pursue them and delivers a near fatal magic blow to Sheik. While trying to help an unconscious Sheik, Link notices the crest on Sheik's hand. Together, Link and a rescued Nabooru fend off the other Gerudo, allowing Link to escape on horse with Sheik.
- When Sheik reveals himself as Zelda, Link learns Zelda's backstory. While on the run, Zelda decided to disguise herself as one of Ganondorf's male minions until Link returned. Impa made her appear as a Sheikah descendant. They share their tender moment, but Ganondorf then captures Zelda, revealing how she let her guard down but he knew she would appear if he let the hero wander around.
- Following the final battle and reunion with Zelda, Link wants to stay with her and rebuild Hyrule. She says she must send him back and close the gateway between them. Link argues he fought for her, not because he was drawn to conflict, but she asserts that this time period doesn't need a hero and he needs to return to the forest. Link kneels and vows that he will protect her and Hyrule no matter the time nor place. As Link ascends to the sky, Zelda says her goodbye and tells him: "I love you."
Did I miss anything? Leave a comment!
Source: Zelda Informer