Here's my attempt at making some sense from the Downfall Timeline.
Title: Deja Vu.
Characters: Navi, Link, Zelda.
Summary: She won't let the Hero fall again.
Deja Vu
When the Great Deku Tree called her, she thought that he was finally assigning her to be a Kokiri's guardian.
He did, technically, but he also assigned her to be a guide for Hyrule's last hope.
She has been rather unlucky all her life, she just never realized how much.
He told her that the affair won't take more than few weeks, and that he'll assign her to another Kokiri afterwords.
She wanted to ask him why was he assigning her to a Kokiri that wasn't a newborn but one that lived fairy-less for years (which was an impossible feat now that she thought about it). She wanted to ask him why Hyrule's fate rested upon a Kokiri's shoulders; the eternal children weren't warrior material at all.
And above all else, why would he assign her to another one after the quest was done with? The bond between a guardian fairy and her charge was supposed to be eternal and not temporary.
She chose against asking eventually; the Great Deku Tree wanted her to summon the Boy Without A Fairy, her charge, immediately.
So she flew around the village, greeting the children as she headed towards her charge's house. He was sleeping, which was odd considering it was rather late in the morning, other Kokiri were up and about hours ago. She circled around him, trying to wake him up but to no avail.
"Can Hyrule's destiny really depend on such a lazy boy?"
She paused, not even noticing that her charge finally woke up.
Why… why do I feel like I said this before?
Her charge, Link, was quite a darling to be honest. He was quiet and polite. She guessed that Saria, a well-known Kokiri, had a positive influence on him.
The boy was obviously happy to have her around, and her heart broke when she thought of what the Great Deku Tree had told her before.
Maybe I can convince him to let me stay as his guardian after this matter is dealt with.
"Navi," she heard Link call out, pulling her away from her musings.
"Yes?"
"Thank you… for choosing me."
Something akin to grief consumed her upon seeing his small smile, so innocent and oblivious. She felt horrible about their destined parting if the Great Deku Tree refused her request. She felt horrible about dropping the weight of this quest on Link. She felt horrible about this entire thing.
Maybe her mind was playing tricks on her… but she had a feeling that something bad was going to happen soon.
"Navi?" Link called out again, puzzled about her strange silence.
"Ah… you're welcome, Link," she replied, resting on his head.
Let him stay happy for now, part of her mind - one she didn't know she even had - pleaded.
She felt sick.
For all their efforts, the Great Deku Tree couldn't be saved.
They thought that by defeating the fiend which caused his suffering, they could lift the curse that was placed on him. But the fact was… they couldn't save him.
So she and Link decided to fulfill the will of their caretaker, to go and help Princess Zelda and Hyrule.
She watched as Link said goodbye to Saria, promising that they will remain friends no matter what happened.
Link ran, ran before he said that he didn't want to do this, that he didn't want to leave his only home.
And even though Navi was his supposed guardian, she couldn't comfort him when she thought the same herself.
"You really do know about everything," Link remarked, a childish awe evident in his voice.
Their quest for the Spiritual Stones - that Princess Zelda was the one to set it on motion - was finally about to finish. They encountered all kinds of unique people: like Darunia, who formed a brotherly bond with Link upon witnessing his heroics; Ruto, who wanted to form other type of bonds with her charge (she had to explain what marriage meant to him, a tiring experience to say the least); the people of both Castle Town and Kakariko Village, who were quite… odd to say the least.
They also faced a lot of enemies, enemies that she knew quite the information about for a forest fairy. Sometimes, she could even predict the moment one of them was going to attack.
It was strange and alarming, yet she didn't pay any heed to it until Link's innocent remark.
"I had a lot of time." She shrugged, trying her hardest not to show her concerns.
This knowledge doesn't make sense at all.
Unfortunately, she didn't have more time to ponder about it.
The castle was under attack.
It was strange how the simplest of things caused the most damage.
A simple song, and the door opened for Ganondorf to take control.
A simple song, and Hyrule was to suffer years of hell.
A simple song, and neither Link or her was ever the same.
A simple song ruined everything.
Seven years had passed, and they were again on another quest.
It was a shock to see what happened to Hyrule, for it was a beautiful kingdom to their eyes not so long ago.
Nothing will ever feel worse than seeing Link's innocence dying with every moment. Losing his best friend to sagehood and then learning that he wasn't a Kokiri but a Hylian with no family out there (suddenly, the Great Deku Tree's words made awful sense) all at once was overwhelming, down right maddening even.
But Link continued on without stopping, without questioning, and she wondered why.
Was it because he felt it was the right thing to do? Was it because he still thought that he didn't finish his original quest?
Or was it because he had nothing to return to?
And so they continued on, awakening a sage after sage, Link losing the people he had met years ago one by one, and slowly cleansing Hyrule from Ganondorf's influence.
The 'Knowledge', as she decided to refer, increased with every happy or terrifying moment, but she still refused to acknowledge it, afraid of what she would discover.
That is, until the Shadow Temple.
"Help… me…"
"Did you hear that, Navi?" Link asked, stopping in his tracks to listen to the pained pleas. "Doesn't this voice sound familiar to you?"
"Please… help me…"
Navi frowned, not liking this at all. "Yeah, but wh- the kid at the graveyard! Didn't we see him when we went back in time?"
Link's eyes widened in horrified realization, quickly searching for the source of that voice.
But why would the kid's voice remain the same seven years later?
Before she could even voice her concerns, Link ran towards a hidden room. "Link wait!"
It was too late for that; something covered in the darkness of the temple caught Link off-guard, injuring his left arm before he could even realize what was happening.
She couldn't tear her eyes from the deep wound that was inflicted upon her charge as he fought his assaulter, killing it eventually. "Drink your potion, Link."
Link didn't seem to hear her. "Was that…?"
"No," she answered quickly, not even bothering to think of the matter any further; Link already had enough on his mind.
"Drink your potion, Link," she repeated.
This time, Link heard her.
The road to the Spirit Temple was rough, and she could excuse Link's apparent exhaustion on the desert's trails.
She excused everything but one: the wound was still bleeding. "You should take a rest, we can head to the temple afterwards."
Link shook his head, an oddly cheerful smile playing on his lips. "I'm fine, Navi. It's just this one temple and everything will be over. I promise that I'll rest after clearing it, okay?"
"Okay…" she agreed against her better judgement.
And then it was over.
Link was finally facing Ganondorf, and much to her eternal frustration, she couldn't help him.
To see someone she guided and helped on a seemingly endless quest and being unable to help him at last part of it enraged, terrified and saddened her all at once.
But she tried to stay hopeful and greet her charge, her boy, with a smile the moment after his victory.
That moment, however, never came.
"LINK!"
It took one moment, one wince caused by that damned wound that refused to close no matter what, one pained gasp for the Hero to fall.
Ganondorf's power grew out of control upon defeating him, destroying everything in his way. The princess, freed from her captivity as a result of Ganondorf's rampage, took her away from Link and ran.
Only one thought haunted her mind at that moment.
"It's my fault."
The princess's face was like carved stone, but her running tears told of her despair.
"I'll send you back." She raised the ocarina she took away from Link to prove her point. "Please, warn me… warn him."
Navi nodded, too shell-shocked to question her request. "And you?"
The princess only smiled sadly and played her lullaby, but before she could reach the final note, Ganondorf, or whatever monster he turned into, found them.
She sent her back, indeed, but it was incomplete.
Everything made sense.
This odd knowledge she had, the fact that the princess thought Link's name to be familiar upon their first meeting, Link's strange dreams, the fact that she felt like most of the days she spent with Link were a repeat of events that have yet to happen.
This wasn't the first time she faced this, and if she didn't intervene now, it wouldn't be the last time.
"Did you hear that, Navi?"
She won't let the Hero fall again.
"It's nothing Link, just continue on your way."
Link looked unsure for a moment before he shrugged and did as he was told.
This time, the Hero won.
End.