A phrase often used when someone asks what/why someone else is doing when confused, or moral is in question. The phrase is then used as a response to further confuse/annoy the person asking.
The phrase was turned into a meme though mlp:fim
with the character rainbow dash
who had a "deal with it" not caring attitude when ever she put on random sunglasses that she would pull out of nowhere.
fluttershy: ...um rainbow i don't thin...
rainbow dash: (sunglasses) Deal With It!
fluttershy: um okay...