If the box is the type that has everything internal (no external 'levers' on the side) then you should be able to stick a screwdriver in the hole in the top, (I'm assuming the shifter is completely gone), and shift it into neutral. Just shift stuff around until you get it. Is the box still in a car? Then depress the clutch, or rock the car back and forth without the clutch (brakes off) as you try and shift. Beware of the car rolling away as it goes into neutral. If the box is out of the car twist the output shaft back and forth while you try and shift.
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. There are probably three levers on the side of the transmission. Use those to shift to whichever gear you want.
Press the clutch.
Yeah, that's about it. Unless you've got a fly-by-wire system and have software which will talk to the car's computer on that level.