Im using 16.04 with gnome and I used katoolin to install some programs. Well after a reboot when I tried to install pidgin every shows up as if I was using kali. Is there a way to make ubuntu my base system again? Or is there some thing else causing this problem.
Since Kali is not supported on this site, the best we can really suggest is to reinstall Ubuntu clean. You can take steps (like making a backup before you start) to preserve your personal files in /home, but the changes that will make everything show up as if you were using Kali are pervasive enough that reinstalling will be the most efficient way to fix your system.
Then, if you wish to experiment with Kali, install it in a separate volume, ideally with its own /home separate from that for your Ubuntu Gnome installation.