MAJOR FtNW SPOILERS FOLLOW. AS WELL AS A HERD OF DEER.
FtNW: short on story (not to bash, i <3 it, but it is brief in some spots). Long on possible theorizing. If you ever wonder why I play Awaker the way I do, this should help.
Here is a list of unexplained/strange incidents that happen throughout FtNW. My take on Awaker is based on my interpretation of most of these.
1. The children are killed in a car accident when their father just happens to not be with them. Even though he covers up their deaths--Johnny has never been legally declared dead--Marlow still somehow knows about them to give the offer of his services to Graham, if he assists with the research. Graham just happens to have the resources to spare five years of his life on this quest, and without Johnny ever noticing a drop in his quality of living.
2. Johnny remembers something that happened in the Garland estate while he was dead--and right before his soul was summoned to return. (also notable is that this flashback starts in his old bedroom.)
3. The Malice for the ritual is gathered using "animal skins". So Roger Bacon says.
4. In the ritual, all of the Malice is stored in Johnny's tube until Grace consciously decides to give him her Will, displacing the Malice. Why it was not evenly distributed is never explained in canon.
5. Marlow is killed by a monster emerging from a Window when Johnny meets him. It is never explicitly stated who opened the Window--Malice is bred by negative emotions, but some characters are very calm when they open a Window. Also, if the Window was opened by Marlow, it would be the only time in FtNW that a monster attacks its summoner first.
6. Gilbert sent Johnny to find Marlow. However, he shows no interest in Marlow's death afterwards. His interests are Lady's power and Johnny's in comparison.
7. Johnny first remembers bits about his death after turning into Awaker.
8. There is no canon explanation of how "Awaker" got his name. "Lady" got hers because she could not remember her name to give Killer, and he had to call her something--obviously this isn't the case with Johnny, since his teammates already know his name.
and now, ~explanations~:
1. This is too fishy for coincidence. How did a black magician eager to prove his talent just happen to find a rich businessman willing to fund his research? He created the opportunity by murdering the father's beloved children.
2. Johnny was in the house before his soul was summoned because his spirit was -always- there to begin with. For whatever reason--probably a sheltered child's fear of being alone--his soul made its way back to the house.
Of course, his father would be unaware of a supernatural presence. None of the Garlands had any sort of spiritual powers until after the twins' resurrection. This means Johnny's soul would actually be 21 years old, and he spent 5 years alone, perhaps watching as Marlow did his testing, perhaps even experimenting on the twins' corpses. Marlow could probably communicate with Johnny, but going with #1's explanation--that he murdered the twins--it's unlikely they would have much to say to each other.
3 & 4. "Animal skins" seems an odd explanation for the Malice for two reasons. First, Malice was explained as being created by emotions. What do the skins by themselves have to do with it? In Koudelka as well as SH1, corpses are used--but the notable thing is that all the corpses are of murder victims. Unless the game is condemning hunting (which doesn't seem likely), it seems odd that just animal skins are capable of creating the necessary Malice to resurrect two corpses. (For reference: in Koudelka, Elaine's resurrection required approximately 300 murder victims. That's 300 corpses to animate just 1.) Also, the house was abandoned shortly after the resurrection ceremony, yet these "animal skins" are nowhere to be found when Johnny and his friends come back to check it out. Who would've moved them?
On the other hand, the series has before had spirits that are very powerful on their own due to their hatred and misery: Charlotte, also from Koudelka, is a notable example that can take on a twisted form. Guess what, people? There's an angry, lonely spirit in the house. It's Johnny. This also explains why all of the Malice is drawn into the tube with Johnny's corpse--it's his to begin with.
5 & 6. The monster tries to attack Johnny after eating Marlow, so no matter who summoned it, it eventually does turn on its summoner. However, people are willing to deliberately summon monsters in-game, which suggests the monster would only attack the summoner if they are the only one left. This would point towards Johnny being the one to open a Window. He couldn't have done it consciously, since he doesn't remember the ritual at that point--but it's notable that his expression changes, becoming rather unpleasant as he approaches Marlow. Why? Well, Marlow is being a trifle difficult, but usually Johnny's initial reaction to that is a bit of awkwardness and a little shyness. Not irritation right off the bat. This especially seems strange when he was laughing shortly before. Maybe he's remembering something unpleasant...?
This would also fit in with why Gilbert sent Johnny to find Marlow but isn't interested in him afterwards; Marlow was only supposed to serve as a trigger. Because Gilbert knew about the ritual and its circumstances, he knew Johnny would harbor ill feelings towards the man, to an extent that no one else would be able to elicit from him very easily.
7 & 8. And here we reach the destination of the magnificent teal deer: Johnny and Awaker are the same person--and at the same time, they aren't.
Johnny is a 16-year-old (17 in Disc) who loves life, loves being around people but is anxious about being left alone to the point of being ridiculously eager to please (THREE WEEKS WALKING TO THE GRAND CANYON FOR A NEW CRUSH???), hates confrontations, and tries to avoid problems when he can.
Awaker is the ghost of a 13-year-old boy who died and watched his murderer toying with his and his sister's corpses, who saw his father standing nearby but never acknowledging his presence, and who eventually went insane and lost awareness of even being "Johnny" because of the Malice. (If you asked him what he is, he would probably answer that he's Malice itself. He's wrong, but hey. He's only human mortal crazy.) He clings to life to the point of being willing to kill anyone who threatens it, is distrustful of others, and thinks the solution to everything involves someone else's pain. He's also scornful of Johnny, the "corpse", and thus wants to be acknowledged by another name.
There are possibly a few similarities between them--for example, both hate being thought of as childish (because they were young and defenseless when they first died), manifested in Awaker's adult appearance--and yet they both betray themselves; Johnny's insistence on not being called a kid makes him look childish, and the origin of Awaker's name (at least in my head) is a commonly known children's song. Otherwise, though, their paths broke off at the point of their first death, and they became radically different; then, suddenly, their paths reconnected at the second death, and there's been tension ever since.