So most of the characters are Doctor Who ones, but it centers on the Torchwood story... xD
The Doctor's speech is partly inspired by the emotion in the Doctor's speech in the episode The Doctor's Daughter.
EDIT: Now uploaded with correct grammar. The tense was hacked up in the end. I used past tense and then I realized I switched to present tense after the Doctor's monologue.
A crater. It was a big, smoking crater. Well, not exactly smoking anymore. That had cleared up days ago. But truth be told, it was a crater. And on the edge of it stood United Nations Intelligence Taskforce New York sector medical director Martha Jones-Smith. Mickey stood next to her, holding her hand. Martha had been sent over by UNIT headquarters in America to survey the aftermath of the 456 in the fellow NATO country United Kingdom because of her original nationality. That, and because of her ties with Torchwood.
And Martha Smith nee Jones was absolutely furious. Her hand gripped her new husband's hand tightly. A British general came up to her and attempted to brief her on the spot. "I don't want to hear it," she interrupted. Her voice was starting to shake. The general paused and tried to begin again. "I said I don't want to hear it," Martha repeated.
"Just back off mate," Mickey told the UNIT general. The general relented and walked back to his soldiers.
Martha must have stood there for what felt like eternity before she heard it. The groan of engines, the ringing of an alien bell. Mickey heard it too as they both whirled around, facing the bay, where something blue materialized into view. British UNIT was astounded as well.
A man stepped out. A man with brown hair and a matching brown pinstripe suit. He wore a tie stripped brown and white as well. Hands in his pockets, he approached the explosion site with a defiant look on his face. Martha looked hopeful, even though she knew the Doctor would do nothing about it.
After nodding to Martha and Mickey, he crouched down at the edge of the crater and released his hands from his pockets. In the process, he pulled out a stopwatch and set it at the edge of the rubble. Then he let out a breath, standing up and turning around. His hands were slightly formed fists at his side.
"Let this be a lesson to you," he began with a menacing and commanding tone. He addressed the British generals. "Let this teach you the capacity of humanity's terrors. And learn. Learn from your downfalls and weaknesses, your mistakes and frailty –fragility. Because this had to happen in order for you to learn. And as you learn, the human race will become stronger and greater. It will span across the stars and solar systems. It will triumph as an empire. And learn from one man. From one brilliant, fantastic man…"
The Doctor's voice cracked. "A man who had changed for the better. A cursed man who is on a mission to destroy a planet, to destroy an entire species. A man who is bent on revenge and will commit genocide. And you know what?" the Doctor asked. No one answered. They thought it as a rhetorical question.
"Do you know what?" the Doctor shouted. "I am going to let him. I won't be there to stop him. And I will have no regrets on that. Why? Because the blood is not on my hands. It is on yours. From now until you die, remember that. Remember the blood of an entire species invisibly staining your hands. Because that is what you did. You tore away his sanity. You're government wanted to eliminate Torchwood? It is as good as gone now." The Doctor swallowed hard and spoke once more.
"Faraway, billions of years in the future, Jack Harkness is alone in a room. And just outside that room is dead, decaying bodies. Just skeletons. Outside, the people are mourning and trying to escape the quarantined planet of New Earth. They've longed to see the sunshine again. To feel the light. And Jack Harkness makes that happen. He brings in life and light again, giving his own life in the process. He dies his final death as hero, not as a murderer or a con-man. What will you die as? Because right here, right now, I only see two heroes."
He casted a glance at his former companions and motioned for them to join him in the TARDIS. As the doors closed, Martha promptly broke down as her husband held her and the Doctor looked on, helpless. Then the Time Lord set the controls for New Earth, giving Martha and Mickey the last moments they'd ever have with Captain Jack Harkness.
When it was time for them to leave, the Doctor again ushered his companions back into the time ship. He took one last stroll up to the glass jar and placed his hand on the physical error that separated him from the Face of Boe. Looking in the Face of Boe's eyes, the Doctor opened his mind completely. He poured out his apology and sympathy –the pain he felt in both of his hearts for his old friend. "I'm so sorry," he whispered. There was no reply as the Doctor stood up to leave.
Right as the Doctor's TARDIS started to dematerialize, the last of the Time Lords swore that he heard three words echoing.
I forgive you.