Merlin has been suffering from terrible nightmares every night, dreams where his secrets are revealed and something horrible happens. This, coupled with the fact that magic is still not accepted in Camelot, makes him start to lose faith.
He begins to withdraw into himself, closing himself off from all others, being a good, quiet, normal servant, and nobody can stand it.
So Magic takes things into its own hands, and they begin watching Merlin's past from the day he arrived at Camelot. Perhaps Merlin will heal, and perhaps he's be destroyed. It's a desperate gamble, but Magic has nothing more to lose.