[Blue)(Fusion]

You have either a bad Coil-On-Plug (COP) or a dirty spark plug.

Pull all of the spark plugs and check for contamination. Oil on the plug will prevent it from firing and will also indicate poor valve stem seals or piston rings. Fuel on a plug will indicate that the plug is not firing. If everything on the plug itself is okay, than the COP that was on that plug is bad and needs to be replaced.

Since you're halfway there you might as well replace the plugs with some new Motorcraft ones. Make sure they are gapped to .054". Do NOT use anti-seize when installing spark plugs! Torque plugs to 16 ft-lbs with no anti-seize or oil on the threads. Apply a liberal amount of dielectric grease to the ends of the COP boots to prevent moisture from getting in.

Regarding the black oil, are you looking at it while cold or hot? My oil looks pretty dark when cold (but it's below freezing here lately) after only 1,000 miles, but when hot it's a golden brown, not much darker than how it poured out of the Motorcraft bottle. If it smells strongly of fuel, this would support that there is atleast one cylinder not firing and the fuel injected into the cylinder is getting past the rings and into the oil.

Once you fix the misfire, change the oil and filter to get that fuel out of there. Be sure to use a Motorcraft FL-820S oil filter or equivalent with an anti-drainback valve to protect your engine on startup!