So, in one sequence nearing the end, I believe Alan gets swallowed up by the darkness and Thomas Zane comes by in his diving suit to help him out.  At this point, Alan sees a mirror image or clone of himself, just staring at him.  And then Thomas Zane, in his weird Big Daddy voice, says "Don't mind him.  He's Mr. Scratch."
 
I have no idea what this means, and thus it's probably my favorite part of the game.  A lot of the stuff in the game was too understandable; the lady of the light, Hartman, and evil lady Jagger... I could have it be more insane and out there.  That's probably why I liked the Mr. Scratch line.

I was figuring that by fixing the story Alan would no longer be part of it.  He would once again be outside of the story so Mr Scratch was there to take his place.  Maybe.  I just finished the game and I'm still processing what happened.   
 
What I thought was a little weird was that when he said "Mr. Scratch" I didn't hear the word 'scratch' I just got a sort of 'sc' sound then static.  I only knew he was Scratch from the captions.  I thought that was interesting but I wasn't sure if it really happened or if I just misheard it.

Yeah I don't get this either. It seems kind of out-of-nowhere.

@Phunk_King

" I was figuring that by fixing the story Alan would no longer be part of it.  He would once again be outside of the story so Mr Scratch was there to take his place.  "

Yeah I can't believe how people talked about the product placement. If nobody'd mentioned it, I literally wouldn't have noticed.

This might enlighten a bit 
 
http://en.wikipedia.org/wiki/The_Devil_and_Tom_Walker     
 
Mr. Scratch is the replacement of Alan Wake, taking his part among the writers friends and wife, taking his place in his own life.

One of the guys from Rememdy commented on the "game club" that Kotaku posted a while back saying that we will learn more about Mr. Scratch. Be that through DLC or a sequel, I don't know, but I look forward to knowing more about this one, it was definitely very weird and the fact it wasn't dwelled upon for very long only makes it more mysterious.

" One of the guys from Rememdy commented on the "game club" that Kotaku posted a while back saying that we will learn more about Mr. Scratch. Be that through DLC or a sequel, I don't know, but I look forward to knowing more about this one, it was definitely very weird and the fact it wasn't dwelled upon for very long only makes it more mysterious. "

" @Jeust:  Really? I never knew that. Intereseting. I hadn't heard much of what the DLC was about.. But even still, there's going to be more than one so they could do on with Mr. Scratch at any time they liked :) I just hope they shed at least a little light on him (pun most definitely intended) before the sequel. "

 He basically is an avatar for Thomas Zane, in a similar way as Barbara Jagger was to the Darkness. It's about keeping the balance. :p "

" @Jeust said:

 He basically is an avatar for Thomas Zane, in a similar way as Barbara Jagger was to the Darkness. It's about keeping the balance. :p "

That's an interesting way of looking at it. Sounds like a good explanation to me :) I can't wait for any of the DLC to be honest, expanding on this awesome story will be...Well, awesome? :)  "

That kinda makes sense. That's why his name was all scritched out: because he's bin edited out of the story.  edit- MAYBE Alan edited himself out of existance. That's why he was talking about balance and losing/gaining things at the end there. Maybe he sacrificed himself to bring back Alice- Which is why Alice crawls out of the lake alone at the end. Maybe that's what Thomas Zane did aswell, which is why nobody's ever heard of him.  I don't know, this game hardly makes any sense. "

Mr. Scratch is the novelized version of Alan Wake. Alan Wake is stuck in the cabin and you only play as him in the very beginning. Everything from the car crash on is Mr. Scratch, who is the version of Alan that Alan is writing in the story. It's all a story that is being manipulated by Barbara Jagger in an attempt to give the darkness power, but the TVs are Alan's 
subconscious trying to make him realize that it's not real. The DLC delves further into this concept.

" Mr. Scratch is the novelized version of Alan Wake. Alan Wake is stuck in the cabin and you only play as him in the very beginning. Everything from the car crash on is Mr. Scratch, who is the version of Alan that Alan is writing in the story. It's all a story that is being manipulated by Barbara Jagger in an attempt to give the darkness power, but the TVs are Alan's  subconscious trying to make him realize that it's not real. The DLC delves further into this concept. "