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1. Where was it said that Dethrix was loyal to the Stranger? To my recollection, AQW told us that Sepulchure was never intended to become the Champion of Darkness. In fact, Artix was "created" to take that title away from him. (Again AQW.)

2. While I think it is good to see you've come to understand 50 years would be way too long considering Drakath and Robina this still leaves us with Gravelyn. She's 2 years in DF when we first see her and Lynaria can no longer give birth to her.

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Being a Doom Knight, Dethrix was loyal to the Mysterious Stranger in a manner similar to Sepulchure. He searched for power and was granted it in the form of the Doom Knight Armor, although his purposes hadn't been quite as pure as Valen's had been.
I hadn't thought too much on the Champions, to be honest. That subject doesn't seem to hold a great deal of significance in Dragonfable, and so I didn't think it would be necessary. This is, in many ways, a retelling of Sepulchure's backstory for Dragonfable. Though Sepulchure had thought so during his time in Dragonfable, he was never intended to be any sort of champion. The Mysterious Stranger only used him to carry out his own plans of annihilating Lore.
As for Gravelyn, that initially caught me off-guard, but I now have an interesting idea brewing. :D

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Just wanted to note, according to The Span Champions don't actually exist in DF. For whatever reason instead of Avatars or Lords, AQW has the (muuuuuuuch weaker) Champions which serve a similar (I assume) purpose. The driving force behind them seems to be the Elemental Planes in this case.

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Gravelyn is not really the child of Lynaria. Rather, she technically is Lynaria.
After the night where Sepulchure eliminates the Rune Knight Order (Which, I had forgotten to mention, marks the very first Friday the 13th), there is still a small, shriveled fraction of Valen left inside of him. It is that dwindling essence of Valen that attempts to conjure whatever remains of Lynaria's soul, and in the same manner that Vayle had captured the soul of her brother, Edgar (Sealing it in a crystal). However, he is only partially successful. He's only able to capture the purest and most distinct portions of her soul, devoid of any darkness that may have lingered deep in Lynaria's spirit.
In Dragonfable, Sepulchure would use this crystal and the power of the Fire Orb to "rebirth" Lynaria in the form of Gravelyn, a perfectly healthy human that happens to be an embodiment of the purest parts of her soul. This is why, even in Dragonfable, she would react negatively in the presence of darkness and be unable to wield it herself. This is also why Sepulchure is so intent on defending Gravelyn despite the fact that his ruthless nature conflicts with such affectionate behavior: the little portion of Valen that remains is defending Lynaria, even in their respective "deaths."

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On another note, I take it Faerdin represents the "main protagonist of DF" so why didn't he act upon meeting the Stranger outside of Falconreach?

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I hadn't expected anyone being able to guess that I'd make use of magic that had been referenced in Dragonfable so long ago. ;)
As for the second part of your post, Faerdin is not the Dragonfable Hero.
Rather, he sets up the event that leads to the Dragonfable Hero rising to power. It will be implied that he is responsible for having located and secured the White and Black Dragon Boxes. During the first two Books of Dragonfable, Faerdin is in hiding. In Book Three, however...

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I don't know the story about the Black Dragon Box, but the White Dragon Box has been mentioned to have been recovered(?) ages ago. It was located at the Temple of the Four Winds back when the Prime Wind Orb was still held there.

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Where was it said that the White Dragon Box had been recovered ages ago?
Come to think of it, having Faerdin recover only the Black Dragon Box sounds less messy and would be more fitting in the end. Either way, he plays a role in the recovery of the Dragon Boxes.

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Kordana in the Hunt Begins! tells us of a priest who came to her hundreds of years ago looking for a spot to hide the Orb.

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I changed one detail. King Alteon and Queen Lynaria have already been married for several years now.
This change would better accommodate Robina and her sisters. ;)

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Considering the change in time placement, the Lestrad we know and love is alive at this point in time, but only a young boy (Around eleven or twelve). The Rune Knight Lestrad would be his cousin. Not remarkably different from the set-up I had before; just means the two are closer in age than previously planned.

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You are most cordially invited to attend the renewal of vows between the good King Alteon and Queen Lynaria of Swordhaven on the first Friday
of October.

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Did you think about a reason why Alteon didn't know who Sepulchure was when the hero told him about his involvement of the kidnapping of the Frostvale moglins?

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The good King harbors some guilt over the events following Valen's fall from grace... He won't be spilling any beans to the Hero unless it is necessary.

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The citizens of Swordhaven do think quite highly of King Alteon.
It seems fate may have other plans, though. ;)