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In the Washington, DC area, having a security clearance is a prerequisite for many jobs, but the actual "holding" of the clearance seems to always be the province of the company for which one works. If I was interested in becoming my own company, how could I go about holding my own clearance and maintaining it?
What forms do I need, what processes do I need to go through?
The Joint Personnel Adjudication System (JPAS) is the database that stores information about clearances. It's managed by the Defense Manpower Data Center. They have contact information and regulation about obtaining access, but it appears that you need to have a position that requires you to hold a job that requires you to access the database and its records. An individual can not request access to JPAS on his own, but must go through the Facility Security Officer (FSO). It's up to the FSO to monitor the clearances of the individuals who require (or no longer require) them and the individual to monitor when you received your clearance, when it expires, and properly submit any paperwork regarding status changes that impact your clearance.
You might be interested in the Defense Security Service website, which should have some documents available to the general public about DoD security clearance. The Frequently Asked Questions about the Industrial Personnel Security Clearance Process page should address most of your concerns.
The trouble is that a security clearance is always tied to a specific need to access classified material. To my knowledge there is no way to just have a security clearance without have a specific job or contract where you are required to use it. It doesn't work like a technical certification where you pass a test and it is tied to you individually for a period of time regardless of whether you need it.
If you are moving from one contract or employer to another those clearances can be transferred, but technically your employer is required to notify the agency issuing the clearance within a prescribed amount of time to either transfer it to your new employer or cut it off.
So to more directly answer your question: First your company would need a contract with an agency that required you to have a clearance to do the work. Then you would need to work with them to sponsor your clearance.
Long story short: You can't just get a standard form and apply for a clearance for no reason. You need an Government agency to sponsor your efforts and a good business case for why you need the clearance.
With regards to monitoring a security clearance, there really isn't much you can do other than noting when the various background investigations will need to be redone so you can keep your CV up to date as once the background investigation expires it loses any value when it comes to job hunting. You don't get any notification when things lapse and if you interview with someone saying that your investigation is valid and that is not the case they may not want to keep you around for a reinvestigation.
When you leave the FSO may be able to provide you with a print out saying when the relevant investigations were performed for your records.
From your comments to the question it sounds like you really need to be talking to the FSO and having them find out what is going. Likewise, if you are in a certain field then that may help as different agencies can help sort things out better for their own people than trying to take the general approach to the problem.
In summary, if you are currently employee by someone you should talk to your FSO and work closely with them until the issue is resolved. If you aren't currently employed by someone then you are better off just indicating when the relevant investigations were conducted as a lot of issues might get cleared up just by changing sponsors.
To form a company that holds clearances, you will need a facilities clearance. This is a completely separate process from your personal clearance. You will need a sponsoring organization. You don't need a personal clearance for a company you start to get a facilities clearance; it will just speed up the process. If the company you form does not obtain a facilities clearance, your clearances will be managed by prime contractors to whom you sub.
