Can you open it up and then run power to it to listen in on the start up for where the noise is coming from?
It sounds like the fan bearing is going bad and or something has moved and the blade is striking something. This may be a chance once identified for you to replace the CPU fan or get a upgraded heat sink and fan if your case will allow for a larger more powerful cooler. Also use this as a chance to clean and blow out the case and check to see if you can improve air flow. If needed please post pictures of the offending fan and we can make suggestions.