The main characters name should remain unknown for the entire game.

Tex says

First off, is the protagonist's gender already predetermined? We could give the player the chance to choose male or female, and give the character an androgenous name, such as Jesse. Perhaps even the ability to name the protagonist as well, if voice acting is not present(since I detest in games where the dialog simply omits the character's name from the sound clips. Just a thought, though.

I am probably certain that the main character's gender is concluded to be male, as most games of the RPG variety have a male main character. It would be easier since if we gave the option to choose, we'd have to make two different scripts: one with "her" replacing where it says "him" etc.

Personally, I think this should tie in to the protag's power. The game could begin in the alternate reality, meaning he just accidentally activated his power with no knowledge of what just happened. Opening scene gets merits for being disorienting, immediately immersing the player into the special gameplay elements and story, and prevents longwinded cut-scenes/dialogue at the beginning of the game. Heck it could almost be played out like a dream sequence, since I'm certain until the protag gets the hang of his power, that's what it'll feel like.

Interesting! I see it similar to openings from various Final Fantasies. It could begin as sort of a dream, and then when the character "wakes up" (phases out) he's back in his bed at home or something and we sort of trick the player into thinking it was a dream and not reality, or at least anit-reality.

This section should be thoroughly discussed. This can simply be extra information for the player to help immerse him/herself into the game, or it can be the key to his power and a key factor in the story. Thoughts right off the bat: The "other world" might just be in his head, created by some psychological trauma in his past(if the game decides to go the psychological route). Some event(s) in his past triggered a sort of reaction in his mind that allowed him to access a pathway in his mind that generated his newfound ability. Just some thoughts. Like I said, this part has the potential to be of great storytelling value, or it could simply be used to let you know the character better.

Well, we had some ideas about the final conclusion of the game's story. Stuff about psychology, realizations of the universe, etc. etc. I don't think we should simply reveal his power as some sort of hallucination, but maybe some sort of gift that might not ever be explained. It does help him to uncover the secrets of the universe, but as to how he got it? Who knows?

Personally, I think the most interesting would be a voice in his head. We could make the voice anything we want, but that medium would give a seriously disorienting feeling to the player and protag alike. This would keep the player and protag guessing whether or not it was even real.

I actually had an idea as to this. How about he meets his Alter-Self? The Ghost-Twin could help him understand what is going on and explain some things. Some sort of dialogue like:

Main Character: Where am I? Who are you? Why do you look like me?
Alter-Self: I am you, in fact. Well, a version of you. And this place is a version of your world. Or is your world a version of this? It doesn't matter.
Main Character: Am I dreaming? I feel sick.
Alter-Self: Relax. You've discovered a power that has hidden inside yourself for a long time. You have traversed the dimensional wall between two seperate worlds, two symmetrical existences that mirror one another. This is my world, and I have seen yours.
Main Character: ..What?
Alter-Self: I have known my power - our power - for quite some time. And I have been to your reality, as it were. But I could not communicate with you, or anyone for that matter. It seems a physical law, unexplainable, prevents people from my world being seen or heard while in yours. Of course, I am the only one in my reality that I know has the power to Phase.
Main Character: Phase? Is that what it's called? But how could I have Phased here without knowing how?
Alter-Self: The first few times are involuntary, sort of instinctual. You Phase between both of our worlds without knowing until you learn how to control it.
Main Character: I'm losing my mind. ...Control it... I don't know if I want to control it.
Alter-Self: Don't worry. I can help you learn how.

One other idea: What do think, alternate reality monochrome or a moonlight blue(with a sort of wavy effect)? Would be nice to instantly notice a difference when changing b/t realities.

Of course! I had always envisioned it as a ethereal blue, myself.

Zeitlos Eisen says

What is the main character's name?

Depends on how personal you want the character to be. Players could become the character or play the character. If you become the character the storytelling changes as everyone is new to you and you have no past life in this game. If you play the character then npc relationships become deeper.

Zeitlos Eisen says

What is the main setting for the opening? His hometown? A military base? A futuristic mall? What is the name of it?

I like Tex's idea of starting off in the other world. At first I'm imagining a small village/town that resides on the natural land but still has its ironpunk/cyberpunk areas or shops. It would be a midpoint between the natural land and technological land and would be close to a big city that hosts major ironpunk/cyberpunk themes on the technological land.

You could also split natural land for ironpunk and technological land for cyberpunk.

Zeitlos Eisen says

What is his backstory, his psychological make-up, any important events that has defined him as who he is?

Not sure but if we want to stay true to String Theory, the phasing ability is not a psychological hallucination. Sorry Tex :p

I have drooled buckets over this already. By the way, the GDD is up.

Oh and another idea, not related to story.

We should have music come on at certain times like say a big battle going to happen, music should come on to suit it.

I have some metal music I made ages ago which we could use for the game along with disco (-.-) and techno (-.-).