Fan Fictions can be handy for explaining plot holes, but shouldn't be taken seriously if you're talking about the plotline seriously. I'll use the plot in the Jak and Daxter games as an example.
***HEAVY JAK AND DAXTER TRILOGY SPOILERS***
In Jak and Daxter, you play as Jak, who lives in Sandover Village. At the end of his first adventure, they find a Time Gate and they get sent into the future. In Jak II There they land in Haven City, and learn of a man named Mar, the founder of Haven many eons ago. The current Ruler of Haven City is a small child who is being kept secure by The Underground from the tyrannical fake ruler of Haven, Baron Praxis. Jak finds that he was in fact born in the future, as he is the small child and sent into the past.
In Jak 3, Jak meets a man called Damas, the king of Spargus City, a place filled with the banished outlaws of Haven where they try to make a new life. Damas had a son named Mar, and you later find out that this is the child from Jak II, meaning Jak is Mar.
***END SPOILERS***
The debate here is whether or not Jak is THE Mar, or is just named in his honour by Damas. If he is honoured with Mar's name, then it means that there is a big muck up which will have to be resolved in a later game. If he is THE Mar, then he will have to travel back in time to fulfil his destiny and found Haven. There have been numerous fanfics revolving around this potential plotline, and the game was released in 2005 with no resolution to this, not even in the slightest with the racing spin-off, Jak X: Combat Racing. The time travel theory is the most agreed upon, and thus far fanfics have been the only way to tell what happens afterwards. In that respect, fanfictions have been helpful in 'what if' situations, as Naughty Dog, the creators of the game, have neglected thus far to provide a canon explanation.
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I was sad when I found that she left
But then I found
That I could speak to her,
In a way
And sadness turned to comfort
We all go there