Do I have to go through S2 to renew my security clearance? Are there other ways to renew?

As an MP, you need to ensure that every member of your Chain of Command and NCO Support Channel are aware of your situation because no Security Clearance = NDMOSQ. If you received an MOS based bonus, this may affect you adversely as you will effectively be Non-DMOSQ once your clearance expires. Since it will affect your Commanders USR, he/she will have a vested interest in making sure you get in contact with someone.

What do you mean they are unreachable? If it's time for you to renew your clearance S-2 should be looking for you. If they have not contacted you, or are not available go to your BDE S-2.

You can do the background information by paper, but it still has to go through S2. They have to justify why you have to have a security clearance. Not sure why the S2 is unreachable, but you do not want your clearance to laps. If it is does you are qualified to sweep floors. Not only that, everybody down the chain is going to hear about it. So if this is 3 months or less out you need to start letting somebody in your chain know because the 1SG is going to be looking for answers on who screwed the pooch.