20 Most Recent 2003 Yamaha YZF-R6 Questions & Answers

Question edited for clarity. Question moved to model category. It appears to be a known issue. https://www.google.com/search?q=2003+Yamaha+R6+no+spark

It could actually be that the countershaft sprocket has stripped-out the splines that engage it to the countershaft. Take off the cover and have a look at the sprocket. Hopefully it is only the sprocket that is damaged and not the transmission shaft that it mounts to.
Another possibility is that the clutch cable has somehow gotten waaay out of adjustment. Just feel the clutch lever; you should have some free play at the lever. In other words, the first 1/4" or so of lever movement should do nothing except take up a small amount of slack in the cable.
Are you sure it is actually going into gear? Or have the splines on the shift shaft stripped-out? These are the things I would check first. If it isn't one of these, then I predict some major transmission work is in your future.