Silence Will Fall when the Question is Asked
Silence will fall is the main Doctor Who theme from series five onwards. The silence takes its name from a prophecy that when the oldest question in the universe is asked, silence will fall. It was only made clear in The Time of the Doctor what the Silence was hoping to prevent.
The Pandorica and the Exploding TARDIS
The Doctors greatest enemies formed an alliance to capture the Doctor and imprison him in the Pandorica. They only did this as they believed the TARDIS was going to explode causing another big bang and a reboot of the universe.
The alliance didn’t find out what had caused the TARDIS to explode, they also didn’t realise it was already happening as River Song was piloting the TARDIS when an alien force took it over causing it to explode.
As time was falling apart the Doctor managed to escape, he stopped the second big bang and stopped the TARDIS from exploding.
The universe is cracked, the Pandorica will open and silence will fall
Prisoner Zero
Cracks in Time and Space
Cracks in time and space that were caused by the TARDIS exploding.
Some were tiny, some were as big as the sky. Through some we saw worlds and people, and through others we saw silence, and the end of all things.
Rosanna

The Eleventh Hour
A crack appears on Amys wall, eventually it opens up wide enough to allow Prisoner Zero to escape

The Eleventh Hour
The same shape as the crack appears on the TARDIS screen at the end of the Eleventh Hour

The Beast Below
The crack in time appears on the Starship UK

Victory of the Daleks
The crack appears in World War II behind the TARDIS as it leaves

Flesh and Stone
The Doctor and Amy notice the same crack as seen in Amy’s bedroom wall

Cold Blood
Rory gets removed from time, only the Doctor remembers him.

The Lodger
The crack appears as Amy finds her Engagement Ring from Rory

The Pandorica Opens
The crack appears on the TARDIS screen as an unknown voice says “Silence will fall”

The Time of the Doctor
The Time Lords send a signal through the crack in time

The Time of the Doctor
The Time Lords open a crack in space and time
Gallifrey and Trenzalore
Gallifrey is trapped in a pocket universe. They found a crack in space and time on the planet Trenzalore. Through this they asked the oldest question in the universe, “Doctor Who?” if the Doctor told them his real name then the Time Lords will know they found the right universe and return.
The Doctor didn’t want to reveal his name as the Time Lords return would trigger a new Time War. The Papal Mainframe (The Church of the Silence) made it their primary mission to keep the Doctor from telling anyone his name.
It’s all still waiting for you. The fields of Trenzalore, the fall of the Eleventh, and the question … The first question. The question that must never be answered, hidden in plain sight. The question you’ve been running from all your life. Doctor who? Doctor who? Doctor Who.
Dorium

Dorium says about the fields of Trenzalore

Trenzalore after the war in an alternative timeline

The TARDIS on Trenzalore in an alternative timeline

Gallifrey about to be frozen in a pocket universe

Trenzalore just before the war

Ship arriving at Trenzalore to see who is sending the signal

The Doctor and Clara on Trenzalore

The town of Christmas on Trenzalore
The Church of the Papal Mainframe, security hub of the known universe
A signal was coming from the planet Trenzalore, the Church of the Papal Mainframe shielded the planet to maintain the truce between different aliens that had come to investigate.
The Doctor landed on the planet and discovered a crack in space and time. The crack was described as a split in the skin of reality. It was left over from the TARDIS exploding in an alternative timeline. The Time Lord’s were trying to communicate through it.
The question was from the Time Lords, “Doctor Who?” If the Doctor revealed his name to them then they would return to our universe unleashing a new Time War.
If you speak your name the Time Lords will return … they will be met with a war that will never end, the Time War will begin a new, you know that Doctor.
Tasha
Silence will fall
As soon as the Church of the Papal Mainframe found out where the message was coming from they altered their mission, their new cause was silence, they ordered the Doctor not to speak his name. In the time that followed, the Papal Mainframe strove to maintain the peace between the Doctor and his enemies.
If you speak your name the Time Lords will return … they will be met with a war that will never end, the Time War will begin a new, you know that Doctor.
Attention. Attention all Chapels and Choirs of the Papal Mainframe. The siege of Trenzalore is now begun. There will now be an unscheduled faith change. From this moment on, I dedicate this church to one cause. Silence. The Doctor will not speak his name, and war will not begin. Silence will fall!
Tasha

The Eleventh Hour
Prisoner Zero says that the Pandorica will open and silence will fall.

The Vampires of Venice
The Doctor and Rory witness the silence.

The Big Bang
An unknown voice says “Silence will fall”.

A Christmas Carol
Christmas Special
Abigail’s Song is themed around silence.

Day of the Moon
A Silent. Madame Kovarian and others wear the eye patches so they can remember the Silence.
The Kovarian Chapter
During the Trenzalore siege the Kovarian Chapter broke away. They travelled back along the Doctor’s timeline and tried to prevent him from ever reaching Trenzalore. The Kovarian Chapter wanted to make the Doctors death a fixed point in time to prevent him from answering the question.
Ironically the Kovarian Chapter were the cause, they blew up the TARDIS which created the very cracks in the universe through which the Time Lords are now calling.
The Kovarian Chapter broke away. They travelled back along your timeline and tried to prevent you ever reaching Trenzalore … They blew up your time capsule, created the very cracks in the universe through which the Time Lords are now calling.
Tasha

Day of the Moon
“No, I think shes just dreaming”

The Curse of the Black Spot
“It’s fine, you’re doing it fine, just stay calm”

The Rebel Flesh
Madame Kovarian appears breifly in The Rebel Flesh

The Almost People
Well dear. You’re ready to pop aren’t you. Little one’s on its way.

A Good Man Goes To War
Madame Kovarian is hoping to raise Amy and Rory’s child to be used as a weapon in a war against the Doctor.

The Wedding of River Song
Madame Kovarian is captured by River Song and is eventually killed by the Silents.