Your printer actually has two separate systems incorporated into one box; a scanner that converts printed images into digital information, and the printer that does the opposite, converting digital information into a printed copy.
By verifying that a document that comes in digital form prints correctly, that tells us the printer part is working and that the problem lies in the other half of the system, the scanner.
For most multifunction printers, the scanner consists of a bar that has two components built into it; a scanning element that pics up a single line of pixels the full width of the document, and a light source usually on the same bar that illuminates the document so the scanning element can pick up the image.
One other check you can do is to compare the image between one that's placed onto the document glass and scanned vs. one that's fed via the Automatic Document Feeder. The two scans work differently; in the first case the scanning bar is physically moved the length of the paper, while the scanning bar stays stationary when the ADF is used.
If there's a difference in what you see using the two different scanning methods, then you'll be looking at the glass for any kind of obstruction when the scanning bar is in its parked position. Otherwise check for any LEDs on the scanning bar that are out and any kind of dust, dirt or lint that might be obscuring part of the scanning head.
The other place to check would be the flexible cable that connects the scanning head to the rest of the printer; over time with the movement of the scanner that connector could crack or work its way loose.
I'd say check those things then come back and let us know what you found and we can go from there.