My favorite song. I think it is about Raiden, his Jack the Ripper persona, and how he is a 2%er (those who enjoy killing)
Wash away the anger
Here I stand beneath the warm and soothing rain
The droplets falling gently down on the terrain
Wash away the sorrow, all the stains of time
But there's no memory, it's only dry inside
Raiden found a new life in the U.S. and, with love and support (soothing rain), overcame his past as a child soldier (the sorrow, all the stains of time) to live a new life. However, deep down, he feels no regret for the people he killed and realizes that there are no bad memories to wash away; it is his true nature.
In the mud, it's sinking deeper
Into a peaceful life
Raiden cannot deny his true nature and finds it interfering in his goals of a new life. He keeps getting drawn back to killing; he admits it himself in-game with the line about "arguing philosophy with terrorists."
And it will flow, like a flood of rain, pouring down on me
And it will not let up until the end is here
And it will go, through the darkest day, in the final hour
When Raiden finally recognizes his true nature and lets the Ripper out, nothing will stop him from reaching his goal and killing his enemies (the events of Metal Gear Rising, pretty much).
And it will never rest until the clouds are clear
Until I find my dreams, that disappeared
When the dust settles at the end of the game, Raiden is an international fugitive. His dreams of a peaceful life are s***tered, and all he has left is the quest to kill towards some purpose.