Sorry for the Necro, but I got an big idea and I wanted to run it past Fosfor and see what he thought.
It originates from the inconsistancy of F!Naruto possessing his vampiric abilities even though he is human. It was stated the Dark Gifts were from his host, not from Naruto himself. So why did he still have them. It was one of the only things that irritated me about Fateless, since I kept seeing an inconsistancy there.
Well, I was rereading the story for the four or fifth time, when it hit me. A perfectly good reason for Naruto to still possess his vampiric powers.
The Heart of Darkness
It was stated that Naruto had possessed the Heart of Darkness for quite a while and had used it's power at least a couple of times. Then when Moebius tried to eradicate him from time itself, it was stated that Naruto used Moebius own power against him to fuel the Heart of Darkness, which is why he was still alive.
But, what if he still had it, but just doesn't realize it yet. The Heart of Darkness would have been semi-saturated by the power of Naruto's vampiric host. And the lingering power of the host that remained within the Heart could have acted as a seed which had allowed Naruto to access his power on a significantly weakened level. With effort, he could use the seed as a template to rebuild his abilities.
As for how the Heart of Darkness remained in Naruto's possession, it would be the same reason Naruto himself still exists. He used Moebius's temporal magicks to fuel it. The Heart, saturated with Temporal magicks, could have easily carried over. But, Naruto doesn't realize he still has the Heart only that for some strange reason his abilities has transferred. After all, he only realized he still had them when tried to assess where he stood in terms of power. He doesn't know he still has the Heart because he has already dismissed it as a possiblity. He wouldn't realize that maybe by being fueled by temporal magicks the Heart might have become immune to the effects of those magics and might have been dragged along with Naruto into the world of the ninja.
It would also give an alternate explaination for the state of Kyuubi. Naruto's wraith-soul might have consumed Kyuubi's soul but the Heart feed on his LIFE. So instead of being just a soulless husk, alive but empty, Kyuubi is very dead, with only the seal maintaining his power by preventing it from escaping.
As for where the Heart is located, maybe it's still in his chest, but beating because it has been jump-started by his body or an ouside force. Much like in Angel, Angel's heart gets jump-started by an electrical attack and it makes him stronger. The same could be applied here. After all, the Hokage said Naruto almost died. Having your heart ripped out and replaced with one that doesn't beat would do it. One defibulator later, you have a beating Heart of Darkness.
Or you can go the mystical route and have it basically grated onto his soul due to the way it was used. After all, I am sure it was never meant to be used that way.
Whue, sorry about the extensive post, but the idea just blackjacked me and I had to get it down before I lost it. So what do you think?