The difficulty will increase, if they use it to mine Bitcoin. That said, a while ago someone used the strongest computer in the world to mine Bitcoin and they failed miserably.
See this article for more information : http://www.businessinsider.com/researcher-bitcoin-supercomputers-2014-6
Your question has been asked before : http://bitcoin.stackexchange.com/questions/28228/why-cant-they-use-super-computers-to-mine-all-the-bitcoins