The scrutiny isn't so bad. They're mainly looking for illegality or potential for corruption. And even if you've committed illegal acts, so long as you own up to it, and it wasn't in the recent past (5 to 7 years), it's generally OK. Felonies are a different matter, of course.

A secret clearance is an interview, taking fingerprints, interviews of family and friends, interviews of neighbors, a credit check, and will likely require drug testing. Top secret clearances and above lead to polygraphs and heavy grilling, with monitoring for new developments. They're renewed every few years, going through the process again.

Most of the military drone programs would be given to one large contractor like Lockheed Martin or NGIT, with lots of smaller subcontractors. A security clearance at secret level or above takes up to 9 months, costs the company over $10,000, and adds that much or more to that person's annual salary potential, so it's not something they hand out lightly.

Most contracting agencies put a small, already-cleared team on the activities that require it, and farm out most of the work (documentation, mundane code, etc.) to people without clearances. If they need more people with clearances, they tend to get temporary waivers for the duration of the work (90 days or less, for example). Most only see a small part of the whole, and you don't choose your projects; your company does.

These are not good environments to learn complex, high-level things like Friendliness.