Doctor Who: Every Prophecy In The Show - Explained
3. The Prophecy Of The Silence
One of the best things about the Eleventh Doctor's era is that the entire thing fits together as one giant story arc, with some of the mysteries in his very first episode not being fully explained until his last.
In that first episode - The Eleventh Hour - we hear Prisoner Zero mention that "silence will fall", and the true meaning of that line wasn't completely explored until the final stages of Eleven's life.
In Series 6, we learn that the Silence is a religious order, one with a seemingly sinister intent. Then, in the finale episode, the severed head of Dorium Maldovar mentions a prophecy, reiterating that "silence must fall", while also warning the Doctor about Trenzalore, and something called "the question".
"On the fields of Trenzalore, at the fall of the Eleventh, when no living creature can speak falsely or fail to answer, a question will be asked - a question that must never, ever be answered.... silence must fall."
Fans then had to wait over two years for all of this to be explained in Eleven's aforementioned last episode, The Time Of The Doctor.
Here, the Doctor discovers a crack in the fabric of reality, through which the Time Lords are attempting to return to his universe. To make sure it's safe to do so, the Time Lords broadcast the question "Doctor Who?" enveloped in a truth field, to ensure that the Doctor will answer without lying. If the Doctor gives his name, they'll know that they've found the right place, enabling them to return.
We then see the formation of the Silence, a group that's determined to prevent the Doctor from speaking his name. If the Time Lords return, all hell will break loose, so, in a way, you could view the Silence as the good guys, since they're attempting to prevent full-scale war. They have questionable methods... but good intent.
Ultimately, the Silence's primary objective is completed: the Doctor doesn't answer the question, the Time Lords don't return, and war is prevented. Prophecy fulfilled!