Lyric discussion by smartfool17 

Cover art for Mercy Me lyrics by Alkaline Trio

I'm pretty sure that I think this song is about missing/needing something.

And that once the thing he misses/needs is gone, he realizes how much he needs it. Because before he didn't pay much attention to it, or took advantage of it, or even wished for it to leave.

And also I sense a little bit of something that skacore_dude said. I agree that he wants to get on with his life from something.