I would recommend you to play Truth Revealed out of the Spec Ops: The Line soundtrack for this scene.

SPOILER ALERT: IF YOU HAVE NOT PLAYED SPEC OPS: THE LINE THE FOLLOWING WILL a) NOT MAKE MUCH SENSE TO YOU AND b) SPOIL YOU FOR THE BEST GAME OF 2012. BE WARNED, DO NOT PROCEED WITHOUT HAVING PLAYED THE GAME TO THE END.

"Puella Magi! Stand to!"
Dragging steps, stumbling.
"Sayaka Miki. We're all that's left of the Mitakihari Puella Magi."
Step. Step. Step.
"We surrender ma'am, Mitakihara is yours."
A wheezing breath. Coughs, spittle, chunks mixed in. The patter of blood.
"Where. Is. Tomoe."
Her voice is rough like sandpaper, so unfitting for a girl her age.
"Upstairs, ma'am. Where she's always been. Waiting, for you."
As Sayaka Miki stumbles forward into the elevator there is little left to remind her or anyone looking at her of a young girl just enrolled into Senior High. Blood cakes her almost from head to toe as do wounds of all kinds. Stabs, bullet holes, shrapnel, burns, broken bones, bruises, bloody chunks gouged out of her with bare hands or gauntlets of powered armor. She doesn't feel any of it.

As it begins moving upwards, her soul gem sparks and she can hear the voice of her again, the voice of someone she once, in a different life, called sempai with honor and adoration.
"Well done Miki-san, you've done what the witches could not- destroyed the Mitakihara Puella Magi."
A moment of silence.
"Do you feel like a hero of justice yet?"
Sayaka says nothing. She just stares ahead. The elevator reaches it's destination and the doors slide open.
"Please, come on it." says Mami Tomoe.
Sayaka enters with shaky steps, swinging left and right. Her gem sparks again.
"Now that you're here, I want to ask you a question. What did you think when you arrived in Mitakihara... when you'd seen what I had done? Did you think it the work of a madwoman?"
Sayaka is breathless from walking. She wheezes.
"Yeah... I thought you lost your goddamn mind. Or I hoped that's what happened."
"Oh yes, that would have made things easier." comes the answer in her head, squeaky, distorted. "But I wasn't that lucky."
"Are you sure about that?" spits Sayaka.
"I assure you, I'm as sane as you are Miki-san."
As Sayaka stubles up the glass steps to the atelier of the highest penthouse in all of Mitakihara,she doesn't think much. She can finally complete her mission.
"No matter how hard I tried, I could never escape the reality of what happened here."
Mami Tomoe. She is painting, a large canvas in front of her. She is clad in her Puella Magi uniform. The image is disturbing. It shows people's flesh melting, a charnelhouse of bleeding eyes and men and women and children beating each other to death in a blood-crazed frenzy while their bodies rapidly decompose and blood weeps out of every membrane, locked in a pit, unable to escape while black fire licks at them. In the center of the painting, a mother lovingly cradling her child in her arms while she forces a knife down it's throat.
The results of a grief seed bombing, the most horrific invention ever to come from Puella Magi cooperating with scientists.
"That was my downfall."
She applies a few finishing touches, a flame, a tear, a wound.
"There! Finished."
Sayaka doesn't know what to say. She knows this image, it's burned into her mind, never to be forgotten. What she had done. But how did Tomoe...
"What the hell is going on?" she blurts out.
Mami Tomoe just gives her a sidelong glance. "Your eyes are opening for the first time." Then she turns around fully. "It hurts, doesn't it?" She nods at the painting. "Go on, what do you think?"
Sayaka looks at it for a second, then turns back.
"You did this."
Mami smiles, a thin tired smile.
"No. You did."
She walks ahead, circling the painting. Sayaka follows. "Your actions killed 47 innocent people." She stops. "Someone has to pay for your crimes, Miki-san. Who's it going to be?"
She steps behind the painting. Sayaka follows, but Mami Tomoe is not behind the painting. Behind it, there is a large balcony and at the end of that balcony there is a big leather chair. Someone is sitting in it.
"Mami? Is that you?"
"You tell me."
Sayaka steps forward, approaching the chair.
"I'm done playing games, Mami."
"I assure you, this is no game."
Sayaka reaches the chair and turns it around. She comes face to face with Mami Tomoe, deceased. Seventeen years of age, she was taken from us by her own musket bullet to her soul gem and head. The school uniform she is wearing is covered in dried up bits of head and blood, adding to the dry and crusted up look of the dessicated, almost mummified corpse. In one of her hands, there is a still-loaded musket pistol, clenched in dead fingers.
Sayakas eyes widen. She leans forward and takes the gun out of the corpse's hand with a crunch and a clatter of metal. As she gets back up, Mami Tomoe, clad in her Puella Magi outfit, steps forward from behind the chair.
"It seems that reports of my survival... have been greatly exaggerated." she says with a smile and a skip in her step.
Sayaka is unbelieving. She shakes her head, trying to gain distance. "This isn't possible..."
"Oh I assure you, it is." Mamis face sets itself grimmer and grimmer.
"How?"
"Not how. Why?" She looks at her own corpse lying in the chair. "You were never meant to come here."
Sayaka remembers. She remembers reading the paper with her orders.

Recon the outskirts. Leave the city. Telepath back to your superiors from outside the Grief Zone. They send in the cavalry. You go home.

She shakes her head. No. No. "What happened here was out of my control..."
"Was it?" Mami's voice is biting, caustic as the grief fire. "None of this would've happened if you just stopped. But on you marched."
Sayaka remembers.
"And for what?"
Sayaka shakes her head again. She stammers. "W-we tried to save you."
"You're no savior. Your talents lie elsewhere.
She remembers the screams as she cut them down. She remembers the things she has done. She remembers Homura jammed in under that truck, asking for a quick death after she had done what she needed to do to save the Puella Magi's reputation worldwide. She remembers striking, striking, striking. Again and again. She remembers Madoka's words at the bombing site, teary-eyed.

'This is your fault, Miki!'
'Stop right there, Madoka.'
'It's your fault!'
'We didn't have a choice!'
'You turned us into killers!'

She cannot face it. "This isn't my fault."
Mami vanishes into thin air, leaving Sayaka alone on the rooftop with only the corpse to keep her company. "It takes a strong heart to deny what's right in front of you. And if the truth is undeniable..."
Sayaka remembers again. Two rotten corpses haning from a highway bridge.
"You create your own."

'What's wrong?'
'I dunno, she just stopped moving'
'I get it,' Miki said. 'We have to choose.'

She is back on the rooftop and Puella Mami is in front of her again. "The truth, Miki, is that you're here because you wanted to feel like something you're not: A hero."
Madoka smashes open a heavy wood double-door as if it were cardboard, then levels a gigantic machinegun at Sayaka. Her eyes are angry and full of tears and hate.

'You left me to die! You're the villian!'
'Madoka!'

"I'm here because you can't accept what you've done. It broke you."
Sayaka is back in the forward command center, the executed corpses of Puella Magi strung up before her. She picks up something in her soul gem, a twitch. She hears a voice.

'Tomoe? Tomoe please...'
'What's goin' on, Sayaka?
'It's Tomoe. She did it. All of it.'

"You needed someone to blame, so you cast it on me. A dead girl."
Mami Tomoe steps away and into Sayaka's head. Sayaka sees her step before her, a smudged window separating them, the same gun in her hand as the one she killed herself with, as the one Sayaka is holding right now. Sayaka also sees herself, as a mirror image in the window. She dimly realizes that that is her, out outside of her head.
"I know the truth is hard to hear Miki, but it's time." Mami Tomoe's eyes are hard, hard like the blades Sayaka used to end countless lives over the last few days. "You're all that's left... and we can't live this lie forever."
Tomoe levels the gun at Sayaka.
"I'm going to count to five, then I'm pulling the trigger."
Sayaka shakes her head, it's all too much for her, too fast.
"You're not real. This is all in my head."
Mami is unperturbed, the look in her eyes hardens further.
"Are you sure? Maybe it's in mine. One."
Sayaka is getting angry. She waves the gun around, she shakes her head.
"No... everything, all of this, It was your fault!"
Mami does not care. She gives Sayaka a sick smile.
"If that's what you believe then shoot me. Two."
Sayaka is at the end of the line. Her batteries are drained, her muscles contain more lactic acid than a glass of milk.
"I-I didn't mean to hurt anybody..."
Mami is merciless. Her eyes narrow. Sayaka looks down. Her soul gem is swimming in corruption.
"No-one ever does, Miki. Three."
Sayaka sees something out of the corner of her eye. She sees her reflection, how it raises the gun and puts it smack against her own soul gem. She cocks the hammer.
"Four."
Not a breath wasted. Suddenly, Mami's eyes grow softer. A regretful, gentle look spreads across her features.
"Is this really what you want, Miki?"
Sayaka has no answer. She stares at Mami, the gun placed against her own head soul gem, stunned and shaken. Mami's eyes grow hard again.
"So be it. Fi-"
"NO!"

BANG

The gun drops from limp, long-dead fingers.
"It takes a strong heart to deny what's right in front of you." Mami says.
It hits the ground. It shatters into a thousand pieces, then falls apart to the dust that her Soul Gem turned into.
"Stronger than you were." wheezes Sayaka before her arm drops limp to her side, the smoking gun still clutched in a vicegrip.
"Whatever you say, Miki." Mami rasps, condescendingly. Slowly, the glass splinters, more and more. "Whatever happens now, don't be too hard on yourself." The cracks obscure her face, turn her into a kaleidoscope. "Even now, after all you've done, you can still go home." The glass shatters, and drops to the ground.
No more Mami Tomoe. No more dreams. Only a balcony with a corpse overlooking a dead city.
"Lucky you."

Sayaka is done for. The world she had in her head- gone. Her own self-image- devastated. She barely manages to stagger over to the edge of the balcony and grasp the handrail there, leaning over the edge where a thousand-meter drop awaits her. She looks down. It looks...

"What now, ma'am?" asks the puella from earlier, the one with the eyepatch and the weird claws. Suddenly standing behind Sayaka, as if she'd always been there.
"Huh?" Sayaka barely is capable to stand, let alone think.
"The girls are asking, what do we do now?"
Sayaka is not in the mood, for anything, really. "We complete our mission."
"And what would that mission be, ma'am?" The same attentive, loyal tone. Sayaka is not in the fucking mood.
She turns around, angrily. "Just get me the god..." No one there. "...damn" She's alone on the roof. "...telepather?" Just like she's been ever since she entered the tower. Alone. A single, little girl left to fight with her demons. She looks down. Her gem is sparkling clean. It's too bright. She doesn't feel like it. She dismisses her Puella Magi gear and stuffs the gem into a pocket.

"This is Puella Magi Sayaka Miki, requesting immediate evacuation of Mitakihara. Survivors... one too many..."

Sometimes, becoming a witch may be a mercy.
Sometimes, your own demons won't let you.
Sometimes, it may be a good pain.
But sometimes it might not. You ask when that would be the case?
That's something you have to choose all for yourself.