I've been meaning to write a tribute to the Ponds for a long time (ever since I bawled like a baby at the end of Angels Take Manhattan). After listening to the song Goodbyes by 3 Doors Down and watching the Name of The Doctor, I realized I had to add something about River too. These three are definitely in my list of best companions ever. I hope I've done them some justice (and maybe find myself some closure) with this.

Last thing, check out Impossible Oswin's story "Note to Self" to see the rest of the Doctor's notebook.

The Doctor sat quietly in his TARDIS, alone once again. He had left River back in New York. He had tried to go back. After the Angels took the Ponds from him in that graveyard, he had run, with River close behind, back into the TARDIS and charted a course for 1930s Manhattan. It wouldn't take them though. The TARDIS's anti-paradox protocols had kicked in and they had landed on Liberty Island, staring helplessly at the city from the base of the Statue of Liberty. They were so close. So close, but forever so far. River had been forced to physically restrain him from jumping into the harbor and swimming to them. Just to say goodbye, he thought, Goodbye and I'm sorry.

"Sweetie, you can't go back," she'd said.

"It's not fair!" he'd yelled at the universe, tears clouding his vision until the iconic skyline blurred. "It's not fair! Not them! It worked! Their paradox worked! It's not fair! Why couldn't I save them?"

River had tried to wrap her arms tighter around her husband, but he'd shrugged her off and stormed back into the TARDIS, locking the door behind him. He had punched in new coordinates, as far away from there as he could- the last place he'd gone to say goodbye- while listening to his wife banging on the door screaming to let her in.

He remembered how her cries had faded as the TARDIS entered the time vortex.

Now here he was. Alone. Running away again. His eyes burned. There were so many places he'd wanted to take them. So many things he'd wanted to do. Now all he had were the things he wished he'd said and giant holes in both his hearts.

All of these things were banging around in his head, causing him physical pain. He needed them out, but he didn't want to forget. He never forgot. Not any one of his friends. He learned many years ago that nothing good came from brooding over lost friends- or planets- no matter how much it hurt. He'd have to move on. Just like he did with everyone; Donna, Martha, Jack, Rose. Especially Rose. It seemed like everyone left before he was ready, some more tragically than others. The Doctor's memory traveled even further back; to a boy genius, the first of his friends he'd led to their deaths, but he quickly shook it off. He needed to move on again. He couldn't take these thoughts anymore. He needed them out. He fumbled around in his drawer of stuff until he found a pencil and a notebook- he'd always preferred a more old-fashioned style of writing over technology-, and flipped past the notes he left himself until he found a clean page. He began to write:

My Dearest Ponds,

I am so, so sorry. I thought I should start with that because I really, truly am. I never wanted this to happen. Not to you. You know, I've seen a lot of things in my thousand years of time and space and I've met a lot of people, and every single one of them was special in their own way. But you, my dearest Ponds, have touched me in a way that no one ever has before. There are so many things I wish I had been able to tell you, but now it's too late. Even if no one will ever know, I need to get this pain out of my head. I have too many regrets in life. I don't want this to be another one. Not any more than it already is.

Rory, I think I'll start with you. Rory Williams. The Last Centurion. Amy's choice. Good old Rory. I suppose I should start by apologizing for crashing your stag party and your wedding and for kissing your wife and for all those times you died and I couldn't save you. You know what, Rory? You taught me what real loyalty is. Two thousand years waiting outside a box for the one you love is no small task. I wish I had that kind of patience. You taught me how you can never believe that you're not good enough. She always loved you Rory, and, I'll admit, sometimes that made me jealous. I never appreciated you Rory, and I'm sorry.

Amy, talk about patience. Little Amelia Pond, the girl who waited twelve years for her imaginary friend. The little girl that never really grew up. But you taught me that that's okay. Sometimes growing up takes all the fun out of life. You taught me to never stand down- or lose your attitude- even in the face of danger, and you taught me that sometimes I can be someone worth waiting for. Amy, you were the first face this face saw and I'll never forget that. Remember fish fingers and custard? I'm sorry I said five minutes. I'm sorry I couldn't save you daughter at Demon's Run. I'm sorry I couldn't be the man you wanted. To the Girl who Waited, I'm sorry I let you down. You were counting on me to save you and I couldn't. I wish with all my hearts that I could have saved you from those Angels. I never wanted this to happen. I was selfish for bringing you with me and I'll never forgive myself. You've become two more lives soaked in the tears of my travels, and I'm sorry.

Then, the Doctor remembered the other Pond. The one he'd known the longest. The one he'd left in New York. The one who- if he remembered correctly and he always did- would be taking a trip to the Library soon. The one who had blocked away her own sadness and stared at the Angel that killed her parents for him, so he could have his moment of grief. He added:

No, three lives. Melody. Professor River Song. The Child of the TARDIS. Oh, Sweetie, I'm sorry I left you. I'm sorry I'm too much of a coward to stop running and go back for you. I'm sorry that the next time you see me I won't remember you. I'm sorry that I'll never truly say goodbye. Not in the way you deserve. You saved my life at the Library- or you will- and plenty of other times. You taught me that it's okay to love someone and that sometimes it is better to do things in the right order. There's something I never told you, River. The reason why I always caught you every time you decided to jump off a building or out of a starship. The reason why I always took you where you wanted to go. The reason why I kept my promises. River Song, I love you, but now you'll never know.

My dearest Ponds; Rory, Amy, River, I love you all because you taught me how. I will never forget you. You have all changed me, and you know what? I think it's for the better. I love you, Ponds, and I'm sorry.

Leaving the letter unsigned, the Doctor tore out the page, carefully making sure the edge turned out perfect. The TARDIS had timed it perfectly, he had arrived. He folded the letter neatly into thirds, walked to the door, and opened it to reveal a place he'd been to once before.

It really is beautiful, he thought, staring out at the dying star and wondering why he never took the time to look anymore. I bet Amy would have liked it. He knew he couldn't linger, else the past him might notice. He probably wouldn't though. He was busy trying- and failing- to say goodbye to Rose.

The Doctor dropped the tear-stained piece of paper and stared at it through blurry eyes as it fell into the supernova. He watched it disintegrate and felt the same pain in both his hearts.

The hole in his soul wasn't any better and the TARDIS knew that. She would have to force him to take his time and mourn.

After the letter was gone, the Doctor waited another moment to wipe his eyes and straighten his bowtie before shutting the door and walking back to the console."Well then," he asked his one remaining friend, "where to next?"

I hope you enjoyed reading it as much as I enjoyed writing it! Please leave a review. If there's anything you think I should add or if you have any suggestions for future stories I'd love to hear it!