I stored my honda vfr 800 for two years. When I tried to start it, it would not start. It used to work alright before storage. It is quite new. What might be wrong with it?

Have you charges the battery? Is it turning over at normal rate. Have you put fresh fuel in it. 2 year old fuel will present a problem.
Mine would die and it turned out that the regulator / rectifier was shot also it buggered the alternator so need all new bits.
Common misconception is that it's just a faulty battery but can be more serious. Get a sparky to check it out.