"Time to go home." The Doctor gazed at Martha who nodded enthusiastically where she stood by the console railing with Donna on her other side. "Yeah. Home," she replied.
It pained him to see his former Companion so relieved to go home, despite knowing that he couldn't blame her for wanting to do so, after her forced trip to Messaline. She was kidnapped and, as far as he knew (she never said, he never asked) made her way through the deserted landscape alone while he was relatively safe with Donna and Jenny below ground.
After years of formulating apologies and ways to interest her in traveling with him again, this was the last thing he wanted Martha to endure -- another war. This wasn't the way he envisioned their reunion to be, and he's had enough of seeing the people he loves suffer on his behalf. Just hours earlier his own daughter died to save him, and Martha had put her life at risk and had seen thousands die at the hands of the Toclafane during That Year in order to save not only him, but the world. Now's the time to rectify his mistakes and salvage what's left of his broken hearts. He'll deal with Martha's wrath later, because he knows she won't be pleased with what he's about to do.
The TARDIS shuddered as the Doctor changed the coordinates mid-flight while his two passengers looked on in confusion, quickly grabbing on to the nearest coral struts around them. Once he was certain that they had entered the vortex instead of flying towards Earth, the Doctor apologized for the sudden change in course, then cleared his throat before facing Martha.
"Before I take you home, Martha, can we talk?"
The Doctor then looked at his other Companion, whose left eyebrow was raised in a silent inquiry. He ignored her expression and added, "If that's alright with you, Donna. It's just that Martha and I haven't exactly had time to... catch up. Not with everything that's happened." Donna raised her hands in answer while walking slowly backwards to the hallway leading to the kitchen.
"No, of course not. I'll just pop into the kitchen and make us some tea before we head back."
Donna smiled at the two doctors; one looked quite perplexed at the sudden turn of events while the other tried his best to look composed despite the beads of sweat forming above his brow. She wished that she could stay and watch the manic Time Lord fidget his way through his apology (she assumed that was what this was about, considering the many times they had talked about his feelings for, and because of, Martha) : goodness knows that this situation had been a long time coming. Donna said her goodbyes and made her way further into the ship, leaving Martha and the Doctor to themselves. When the sound of Donna's footsteps had faded, Martha turned to the Doctor and gave him the stare she had given the group of Hath who surrounded her after she had reset Peck's shoulder.
"Now then, Doctor. What's this all about? I'm tired, I'm muddy, and I just want to go home." Martha's usually calm demeanor was absent from her tone. At any other time she would have been glad for this opportunity to talk with the Doctor, but after everything she had been through today she was in no condition to "catch up". Witnessing the deaths of both Peck and Jenny had caused her to remember the year the Doctor had rewound: so many lives lost and she could do nothing but watch, in the same way she did today. Martha wanted to grieve for them, all of them, and she wanted to go home.
Before she could continue her outburst, the Doctor stepped forward and held Martha's hand before responding.
"I've missed you, Martha." His voice strained as he spoke.
The Doctor continued, barely pausing for breath. "I've missed you and I'd love you to travel with me again. I never said -- but I've always seen you, wonderful, brilliant Martha Jones. I'm sorry for making you feel like you were second best because you never were." Martha remained silent, her eyes fixed on the man before her. She pulled away and stepped backward, her hands clenched at her sides and her chest heaved in quiet anger. When she spoke, her voice was as cold as ice.
"You always do this."
The Doctor could only gape at her, stuttering in reply.
"Wha -- What? I always do what?"
"This! You say things just to get me to stay. Us -- to stay. I know you've done the same with Donna when you thought she was leaving you for good, she told me so. You come swanning in, promising a whole universe of adventure, but it doesn't always turn out that way, Doctor. Yes, I've seen things I never would've seen if I hadn't met you and I'm thankful for that. But I can't do it anymore. I won't let you do this to me again."
Martha's stinging accusations hit the Doctor in waves; the intensity of the truth became stronger with each subsequent crash. He never knew just how much he had hurt Martha; he'd been so self-involved during their time together that he never realized how much he had broken her. The Doctor stepped forward, causing Martha to flinch, but she stayed where she was, silently daring him to deny her charges.
"You don't mean all that, Martha," the Doctor whispered, more like a silent prayer to himself.
"I do." Martha's voice softened as the last rush of her anger dissipated. She closed the space between them and looked up.
"You don't know how it is for us, Doctor. You pick us out of a crowd of people to take with you and we have the greatest time running around the universe. You picked me, and I came. True, it was my decision, but all those fun and games I had with you came at a cost that I almost couldn't pay. I spent a year out there trying to set things right, and as much as I love being with you, I can't risk putting my family through anything like that again. I can't risk having other people suffer because of my decisions. You understand, don't you?"
The Doctor turned and slumped on to the captain's chair, burying his head in his hands. "I'm so sorry. I never knew -- I never asked you. You're right, you're better off without me." Seeing the Doctor overcome with guilt melted Martha's resolve. She walked slowly to the Doctor and sat beside him, putting her left hand on his back.
"That's not what I meant, Doctor, and you know it. Like I told you before, it did me good, having been away. All that I know to do now I learned because of what I went through with you. I have you to thank for my job and my experiences, and I don't regret having ever been through any of it." The Doctor raised his head and turned to Martha, his eyes glistened with unshed tears.
"Martha Jones, you really are a star. Thank you. You saved the world. You saved me -- so many times." Martha smiled and pressed her right palm on the Doctor's cheek.
"You're welcome, Doctor. That's what friends are for, yeah?"
The Doctor grinned and nodded before hugging her to his side. They sat together on the captain's chair and listened to the soft humming of the engines, neither one speaking. A few minutes later, Donna's head emerged from the side of the hallway, her voice travelling across the room to where they were seated.
"Oi, you two, are you just going to sit there and wait for the tea to get cold? I'm not going to ask you twice to come over."
The Doctor laughed then stood up, offering Martha his hand. "I could do with some tea, before we leave. What say you, Doctor Jones? Unless you'd rather that we take you home now?"
Martha let out an answering laugh and shook her head. "Tea would be lovely, Mr. Smith. I wouldn't want Donna's efforts to go to waste, after all." She then whispered to the Doctor, "I don't think I want to see her get really mad."
"A wise decision, Doctor Jones." He said with a wink. Martha took the Doctor's hand in hers and together they made their way down the hall, momentarily forgetting the goodbyes they will face later on. As they walked hand in hand, Martha's voice echoed in the now empty console room.
"Oh, and Doctor."
"I've missed you too."
The TARDIS hummed in approval.