Shot in the Dark

Personally, I see it as some type of struggle, where the narrator is framed and subsequently placed in the middle of a war, all while missing someone close to him or her. For a full lyrics interpretation:

I've been left out alone like a damn criminal

Going back to the framing, they're basically left abandoned while the "antagonist" of the song does what the narrator's accused of doing.

I've been praying for help cause I can't take it all

The struggle is too much for them, so they've been looking for help in every way possible.

I'm not done, It's not over. Now I'm fighting this war since the day of the fall

Because of the framing.

And I'm desperately holding on to it all But I'm lost I'm so damn lost

They're trying to make it through, but the agony is crippling.

Oh I wish it was over, And I wish you were here Still I'm hoping that somehow

Someone close to them was taken, presumably by the antagonist, and they're still optimistic, albeit hardly, about their return.

Cause your soul is on fire A shot in the dark What did they aim for when they missed your heart?

Not too sure about these lines, but I'm assuming when force failed, the antagonist used "harsher" tactics, such as poison via wording, which has corrupted the friend to the point of abandoning the narrator, who still thinks there's hope.

I breathe underwater It's all in my hands What can I do Don't let it fall apart

They're basically trapped in the position and unable to affect the outside world, even though the public perceives the narrator to affect the outside world in the wrong way.

A shot in the dark A shot in the dark

They're beginning to "chant" it, in hopes that it'll come true.

In the blink of an eye I can see through your eyes As I'm lying awake I'm still hearing the cries And it hurts Hurts me so bad

Nightmares haunt them of the apparent struggle the narrator's friend had to suffer while trying to either escape or resist.

And I'm wondering why I still fight in this life Cause I've lost all my faith in this damn bitter strife And it's sad It's so damn sad

The narrator sees no point in life anymore because the war has taken pretty much everything valuable from them.

...

I feel you fading away I feel you fading away I feel you fading away I feel you fading away

The memories are starting to fade due to the crippling agony that's occurred throughout the song, and now they're starting to reluctantly believe it.