The best place to start was the beginning, and she trusted Sam, so she nodded and decided to start. It was high time he understood...
"There is a piece of Timelord technology called a Chameleon Arch which can rewrite the DNA of a Timelord and hide their essence so even they don't know who they really are," Martha explained. "My first experience with this came when the Doctor and I were hiding from a family of aliens and the Doctor and I had to take refuge in a boys boarding school in 1913. He used the Arch, rewrote his DNA into that of a human and trapped his essence in a fob watch that held a perception filter, the same thing that is on my Tardis key." She had told him about her travels before, mentioned them in some detail,
"Toward the end of my time with the Doctor, the Tardis took us to the end of the universe. Literally. A dying existance and the very last of humanity, struggling to survive under the worst conditions. Refugees of a planet long dead, trying to outrun the oncoming darkness and find a place fabled to be paradise. They called it Utopia." She couldn't smile at this. Not at all. "Among their number was an elderly man named Professor Yana who was working tirelessly to try and launch them all off into space." She looked down at her hands. "Except Yana wasn't who we or even he thought he was... I saw the watch - the same one that the Doctor had, and I started asking questions, thought it was too good to be true, the technology was the same. He was a Timelord. The Doctor wasn't alone anymore...
"The thing is that if you are made aware the item is there, then a perception filter is not as effective, where the watches are concerned they even stop working. And when he opened it," Martha stopped for a moment, trying not to practically spit the words out, "the Master revealed himself. He stole the TARDIS, came up with a plan and was elected Prime Minister using the name Harold Saxon. He used the TARDIS to go back and see what had happened to the refugees, who we thought we'd helped. We were wrong."
"They'd turned themselves into these child-like cyborg spheres with a hive mind in an attempt to find a way to survive the terrible place Utopia had turned out to be. And The Master? He used them. Turned the TARDIS into a Paradox Machine and brought them back home, claiming that Harold Saxon had made contact with a new friendly species. He called them Toclofane, the Gallifreyan version of the boogeyman - and they- being of child-like minds, trusted him, did as he said, and sadly did not know better. We helped create them, by sending them on their way. It wasn't long until the United Nations got involved and UNIT - that's the Unified Intellegence Taskforce - took over. President Winters tried to take over the situation, but was killed by the Toclofane, and from there..." she stopped, pursing her lips. "It was the beginning of the end."
She looked down at her hands, becoming quiet for several moments. It was a painful memory. Watching as Japan burnt. It was painful. But she knew that she had to continue. He needed to understand. "I got off the Valiant," she didn't specify that it was an air ship, but she didn't think of it, "using a friend's Vortex Manipulator, given a task by the Doctor. I left my family behind, they were forced to serve him." she wasn't certain if Sam knew Jack or not. "And the human race was enslaved, forced to build weapons for the Master's war against other civilizations." She pursed her lips. "And to defeat him, I was tasked with walking. I spread the word under the guise of collecting pieces of a weapon that would kill him. And I did my job. My penance. For an entire year I walked... I can still see Japan burning when I close my eyes..." An entire country destroyed. An entire people wiped out on the whim of a madman. It explained everything, her animosity, her distrust, everything.
The story wasn't done yet but she needed a moment to collect herself.