I'm afraid so. If you have disconnected the gearbox by removing the primary drive gears and clutch then it must be something in the engine itself. There are several things it could be from a dropped valve to a piece debris jamming things up. It might be a broken dog from the gearbox, after all it is a 2009 model. I wouldn't like to guess or speculate though; the only way to find out is to open things up and have a look.

You could check the valves/top end though before getting heavily involved in splitting the crankcase.

Some further reading that may be of use:

Read this thread regarding broken gearbox dogs, but as you'll see from reading it, there are almost always symptoms of difficult gear changing prior to the problem manifesting itself.

Also read this thread about premature main bearing wear caused by loose crank nuts. Again though, there are warning sounds (knocking etc.) prior to disaster.

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