Thought I might post this, as I just lost my supercharger and went through some expensive repairs and a couple of weeks downtime. I'll start out with a description of the noises that started and a little background on the repairs.
I have an 03 Electric Blue Cooper S, that has about 48,000 mile on it. Running fine, no major repairs engine-wise, then driving to work one day I hear a loud rattle coming from the front of the engine bay. I've had a similar noise pop up now and then, but every time I checked the oil, it was down about a half of a quart and I suspect the tappets were dry on these other occasions. Once I aded oil, the noise went away.
But not this time. This noise can best be described as a "clacking", noticeable inside the cabin and DEFINITELY once the hood was open. Sounded like a very loud diesel, and coming from what seems like the left side of the intercooler. So I suspected a supercharger issue. However, no warning lights came on and so I managed to limp home.
As I pull onto my home street, the sound mysteriously disappears and I think I'm in the clear. About three minutes later, the temperature gauge pegs and I shut the car off immediately.
Get the car towed to the M Shop in Eagle Rock, CA, this is a shop that if you are in the Los Angeles area, I cannot recommend high enough. I'd been here before for servicing, they are much cheaper than any dealership in the area and they walk you through everything they do. In fact, they are the ones that took the accompanying photos as they went through the repairs. I can't thank them enough for their service.
At this point, the car would not run for more than 5 minutes without overheating, so after a quick check of the thermostat (CHECK!), they dug into the supercharger and water pump assembly:
and found nothing wrong with the water pump but completely stripped drive gears for the water pump attached to the supercharger shaft. Take a look:

This has been covered before, but basically the sealed supercharger sprung a leak and dried out, and the drive gears didn't last much longer after that. Long story short, the gears were NOT serviceable, and so I dropped $1600 on a refurbished supercharger from the dealership (there are no longer any brand new superchargers left in North America, although there are about 660 left in Europe), plus $ for labor and water pump, etc.
On the bad side, the dealership charger a $100 core charge for the old supercharger, and I didn't keep it as the shop advised my that it would be very difficult to sell this used supercharger to anyone, as the single shaft that drives the turbine and water pump was damaged, and they didn't think I could get even $200 for it.
On the good side, to warranty the work, they advised to replace the water pump although they said there was nothing wrong with the old water pump. So I do have a used water pump for an 03 Cooper S for sale if anyone is interested in this, please PM me. I will make my loss your gain.
Okay, just wanted to share the story with this group. Hopefully, this will help others if you hear a similar noise (get towed immediately, they may be able to repair the gears if they don't get shredded too bad), or have a similar experience. 48,000 mile on a supercharger? I am not a happy camper, but the car has been so awesome and I have loved it since Day 1 with no previous problems, so I consider myself a lucky owner of a great car.