I love your last two lines, you do a great job of summing up your piece. My one criticism would be that lines 6 and 7 sound a little awkward. Maybe think about rewording “now pain”?

"dark clouds stained by memories" the use of "stained" really elevates this phrase 

You.

The thought of you saddens my eyes covering them in complete darkness
the life you breathe into me slowly fading away by the second leaving me lifeless
My thoughts are filled with dark clouds stained by memories that once brought me happiness but now pain. 
But my heart still beats loud in the sight of you , lifeless but still the same.

3am pain.