Don't panic.
Get a drop-in bore light similar to this so you can inspect the bore condition:
Bore Light
An indispensable aid for all muzzleloader shooters. Brass light drops down muzzle of any rifle or pistol .50 cal. or larger to brightly illuminate bore interior. Alkaline batteries included.
Barrels can flash rust fairly quickly.
Use a wire brush to scrub out the bore. 20-30 strokes.
Or if you have heavier rust, then follow up with an emry cloth or a mild bore paste.
If the rust is not too bad then a quality bore solvent such as Butch's Bore Shine and 20-30 strokes and patches.
Then pump-flush the bore with a cleaning jag and a patch:
Boil or use about 2 quarts of really hot water along with some laundry soapin a small bucket.
Get glove or towel for one hand to hold the barrel. Remove the nipple and place the breech end of the barrel into the bucket. Wet a patch and place on the jag and run the patch from the muzzle to the breech and pull upward drawing hot soapy water into the bore. Pump flush about 20-30 strokes.
Then dump the soapy water and add hot clean water and pump flush another 10 strokes or so. The barrel will be really hot at this point.
Dump out all of the water.
Soak a patch in 99% isopropyl alcohol and run this patch in the bore and in the flash channel for the nippe threads. The alcohol will help evaporate moisure. Wait a few mintues and then run a couple of dry patches in the bore.
Barrel is still hot/warm, then use a quality lubricant. I use synthetic lubes (Clenzoil and Otis085 Ultra-Bore, B/C Sheath, Etc.)for rust protection and natural lubes (Bore Butter, Wonderlube, Rooster Labs)for shooting (patches, wads and for the field) lubricants. If you do use synthetic lubes then they will need to be removed prior to shooting. A windex/alcohol patch followed by dry followed by natural lubed. Don't forget to clean the flash channel under the nipple.
If you still see rust or pitting, then you may need to repeat the above procedures.
Good luck!
Tahquamenon