The exact opposite of cool. It's NOT cool. Usually said by sarcastic individuals while plotting revenge on whoever has said, thought or done something out of line, rude, disrespectful or just plain fucked up.
***WARNING: If you are the one hearing "It's cool, dude" be careful for at least the next few days if not years!!
Idiot: "Homie, I'm so sorry I talked all that trash to all of your friends and co-workers at that party last night. I was shitty drunk. Hope you still have your job Monday morning!"
Plotting person is deep in thought then replies with a sinister look on their face, "It's cool, dude. It's cool."