After leaving Rensselaer, Cooley attended graduate school at the University of New Mexico and received a Masters of Science in mechanical engineering in 1990 while simultaneously working at the Sandia National Laboratory.

After leaving New Mexico, Cooley worked from 1990 to 1993 at Air Force Wright Laboratory at Wright-Patterson AFB on photovoltaic solar cells and later crystal growth of III-V compounds using molecular beam epitaxy.

He received a Doctor of Philosophy in applied physics in 1997 while working under the supervision of Professor Robert Hengehold.

[12][2] Cooley faced a general court-martial at Wright-Patterson Air Force Base in Ohio in April 2022, charged with three counts of violating Article 120 of the Uniform Code of Military Justice by committing abusive sexual contact.

On April 23, 2022, Cooley was found guilty of one count abusive sexual contact for forcibly kissing his sister-in-law[13][14] after a family barbecue.