What will my doctor do for metatarsalgia? will it ever go away?

A few things: Pain in the ball of the foot can be a frustrating thing- you are trying to heal a part of the body you put a lot of weight on repeatedly each day! antiinflammatory medication, padding in shoes, rest, ice can be employed. Looking at your shoes to make sure they fit well and are not excessively worn. Sometimes, injections or ach supports are needed.

Yes it should : Your doctor will evaluate your entire foot, probably take x-rays to determine if bone problem. May inject the area or pad it or put you into orthotics and start you on anti-inflamatory medication.