It's a malware attack. Whatever you do, DON'T accept any invitations to update your software, such as Flash Player, from those pop-ups. You could be letting something really nasty, such as Cryptolocker, onto your computer.
Download, install and run the free version of Malwarebyte's Anti-Malware, which will probably fix the problem. (If not, please post again):
https://www.malwarebytes.org/free/
NB: When installing, take care to deselect the option to take a trial of the 'PRO' version. When running it, select the 'quick scan' option but don't be surprised when it takes well over half an hour to run. When the scan finishes, click to see the results and then click again to remove everything that's been found.