So, here is the second and final part of the story. Hope you guys enjoy it.

The Waveridder

The rest of the Legends had been waiting for the rest of the team to return for the last hour. When they did, they expected them to return with this Jack Harkness. So to say they were shocked when Rip walked in carrying a red haired woman, Sara and Snart trialing behind them with a young looking dark haired man wearing a bowtie and a blond woman who looked old enough to be Sara's mother was an understatement.

"Uh, Rip-" Ray started.

"Not now, I will explain later," Rory snapped as he walked down the hall with Amy in his arms.

"Sorry about this. We'll just…get out of your way," The Doctor said awkwardly before he and River followed after Rory.

"Um, who was that?" Kendra asked Sara and Snart once the group of four had walked down the hall.

"Like I know," Snart scoffed as he sat down.

"All I know is that there was talk about brainwashing and then Rip was calling that woman his wife and we were attacked. I'm as confused as the rest of you," Sara said annoyed when they all turned to her.


Rory walked into the med bay, worried when he saw Amy had finally passed out. He set her on the bed, realizing his arms and shirt were covered with Amy's blood.

"Gideon, she's been shot in the back," Rory said as The Doctor and River entered the room.

Gideon quickly scanned Amy and began repairing the bullet wound.

"Mrs. Pond has lost a significant amount of blood. She'll need a transfusion Captain Hunter," Gideon said.

"Don't call me that," Rory said with a sigh. "She's the same blood type as Ray. I kept a supply of blood in my office in case we ran into such an event. I'll go get it."

Rory moved to go but was stopped by The Doctor.

"Tell me where it is, I'll get it. Maybe you should clean yourself up, get yourself sorted," The Doctor said gently.

"Doctor-" Rory started to protest.

"Dad, I know you want to stay with Mum, but the last thing she needs when she comes to is to see you covered with her blood. And maybe you could use some time to think. This…can't have been easy for you," River told him.

Rory wanted to protest but, looking down at his bloodstained shirt, at the trench coat he was wearing that he now had a violent urge to set on fire, he sighed.

"It's in my office, Gideon will show you. There's a fridge with blood bags, they're labeled. You'll need at least two," Rory told The Doctor reluctantly.

"There, see? I can handle it. Now go get yourself sorted," The Doctor paused. "It is good to have you back Rory."

Rory smiled weakly at The Doctor before walking passed him and River, heading out of the room.

"Do you think he'll be alright?" The Doctor asked River once Rory was out of hearing range.

"Eventually perhaps. But this is not something you can just get over. Dad has to sort through this on his own," River noted and there was a pause. "Now, don't you have blood to go get?"


Sometime later, Rory stepped out of the bathroom of his bunk, the blood all washed off him. He was dressed in regular clothes now, the damned trench coat thrown aside. As he walked up to a mirror, he paused, looking at himself with new eyes.

The face of Rip Hunter stared back at him. It was perverse, Rory decided, to stare at your own face and feel this level of hatred. He hated this man, this man the Time Masters had turned him into. He was like the worst parts of himself and The Doctor rolled into one. But how much of Rip Hunter was Rory Williams and how much was the Time Masters? These thoughts tormented Rory for several moments before he sighed.

His existential crisis could wait. He needed to make sure Amy was alright.


Shortly after, Rory entered the med bay, finding The Doctor and River watching over Amy, who appeared to be sleeping, dressed in new clothes.

"Gideon gave them to her after the transfusion," River said as she saw her father eying Amy.

"She says she'll be alright. Gideon's no TARDIS, but she's alright," The Doctor noted.

Rory nodded, not saying anything as he stepped up next to them. For a moment, they all just stared at Amy.

"How long was it for her?" Rory finally asked.

"Six months," The Doctor said as he looked at Rory. "How long was it for you?"

"I don't know. They took me to a place where time had no meaning. It feels like lifetimes passed," Rory said bitterly.

"I'm sorry Rory," The Doctor said guilty. "We tried to find you as fast as we would."

"You did, that's what counts," Rory sighed wearily. "How she's been doing?"

"Not well," River said. "At first, we were all on the TARDIS, looking for you. But after two months, we had to take mother back home."

"Why?" Rory asked confused.

"She was becoming careless; she was taking too many risks. She was desperate to find you, whatever the cost. I was worried she'd either burn down the timeline or get herself killed. So I had to sedate her and take her back to your house," The Doctor explained. "We've checked in on her between leads. She's been…struggling."

Rory was silent, processing this. He'd always been insecure about Amy's love for him, especially since finding out she'd run off with The Doctor the night before their wedding. But it was times like today, when she took a bullet for him and nearly got herself killed trying to find him that made him feel foolish for ever doubting Amy's love for him.

"'s called marriage."

The three of them looked down to see Amy's eyes flutter open, the first thing she saw being Rory's face.

"Amy, are you alight?" Rory asked worriedly as he knelt down, taking her hand.

"I'm fine. It doesn't even feel like I got shot," Amy said, staring at him as though he were the sun. "You remember me."

"I do," Rory said as she put a hand on one side of his face. "When you got shot, I remembered when I was an Auton."

"When you shot me," Amy said lowly.

"It was a skipping stone that opened the floodgates," The Doctor noted and Rory nodded, not able to look at any of them.

"Dad? What's wrong?" River asked.

"I did…horrible things. People died because of me," Rory said, remembering Carter's death in guilt. "I was…"

"Like me," The Doctor said sadly and Rory shook his head.

"No, I was worse. You do things for the good of others, even if we may not see it at the time. I did everything in service of myself," Rory said in shame.

"It wasn't you. It was the programing of the Time Masters. Do not blame yourself for what they did to you. You are as much a victim in this as anyone else," The Doctor said firmly as he placed a hand on Rory's shoulder.

"I hope the others feel that way. Because I think I owe them some answers," Rory said with a heavy sigh.


Shortly after, the Legends all sat in the cockpit, waiting on Rip and the three unknown people who had come aboard the Waveridder. Hearing footsteps, Sara looked up and the others followed her lead to see Rory, The Doctor, Amy and River enter the room.

"Captain Hunter, would you care to enlighten us on what has been going on?" Stein inquired and Rory winced.

"It's…complicated. But first, I would like to apologize to all of you," Rory said, taking the Legends aback. "We were led onto this mission under false pretenses, including me."

"Rip, what are you talking about?" Jax asked and Rory sighed.

"First, my name is not Rip Hunter. It's Rory Williams. I'm not a Time Master, I'm a nurse. Like you, I'm from the twenty first century," Rory revealed to their shock.

"Is anyone else getting a migraine?" Mick inquired.

"For once, we're all as confused as Mick," Snart agreed.

"It's complicated. Uh, Doctor, want to help me out here?" Rory asked as he looked at The Doctor pleading.

"Of course. Hello, I'm The Doctor," The Doctor as he stepped forward. "I'm a Time Lord."

"A Time what?" Kendra asked as they all looked at him oddly.

"A Time Lord. I come from a planet called Gallifrey," The Doctor explained.

"You're an alien," Stein realized with a bit of excitement and The Doctor nodded. "This is extraordinary. Once I found out time travel was real, I wondered if perhaps aliens were real as well."

"We are. The universe is more vast than you can possibly imagine," The Doctor smiled, happy to see a scientist among the group. "But anyway, I have a time machine as well, called a TARDIS. I usually travel with an entourage, companions you might say. Rory was part of my entourage."

"Okay, still not seeing what this has to do with us," Ray said.

"The Time Masters," The Doctor said and they gave him their undivided attention. "They have a process of brainwashing. Six months ago from our time, four years ago from your perspective, the Time Masters had a group of mercenaries capture Rory and, once he was handed off to them, they brainwashed him until he believed himself to be Rip Hunter, a Time Master."

"So all that talk about your family-" Sara started as the realization hit the Legends.

"A lie, one the Time Masters made me believe. I'm so sorry," Rory said in remorse.

"But why? Why would they do this?" Kendra asked in shock.

"I believe I can shed some light on that," River said and they all turned to her. "I'm River Song, an archeologist from the fifty first century. In the future, all of you are known associates of The Doctor, who help him in times of great peril. I doubt it's a coincidence that, as Rip, my father chose you as his team."

"Wait, your father?" Ray asked and Sara shot him a look. "Not relevant, got it."

"I think she's right," Rory said, a faraway look in his eyes. "Once I remembered who I was, things started coming back. The missions we were sent on, they were never about Savage. They were about The Doctor; everyone we encountered was a future associate of The Doctor's. I would carry out all the Time Masters' orders subconsciously, thinking I was going after Savage."

"When really you were messing with my timeline," The Doctor realized and Rory nodded.

"So what happens now? These Time Master guys aren't gonna like it when they figure out their errand boy isn't taking orders anymore," Mick pointed out.

"Mr. Rory actually makes a good point. What will the Time Masters do now?" Stein asked.

"Nothing. Leave them to me," The Doctor says, a dark look crossing his face.

The Vanishing Point

The TARDIS materialized into the center of the Vanishing Point. The door opened and The Doctor walked out to see the Time Masters had assembled, wielding weapons that were aimed at him. The Doctor lazily flicked his screwdriver and the weapons sparked as they overloaded. The Time Masters dropped them and The Doctor smiled.

"Hello. It's been a while," The Doctor greeted them.

"Doctor. You have nerve, coming to us here," a Time Master snarled.

"Nerve? No. I wouldn't have even glanced your way if you hadn't come after Rory," The Doctor said and his face hardened. "This is your doing. Perhaps you didn't learn from the Silence, but it is a grave mistake to come at me through the people I love."

"We are not the Silence. You cannot destroy us," another Time Master said and The Doctor smiled.

"Who said anything about destroying you? I can defeat you without resorting to any violence," The Doctor declared.

The Time Masters laughed, their arrogance making them believe he can't back up his words. That was their last mistake.

The Doctor dropped a ball to the floor and it began flashing green. The Doctor waved at the confused Time Masters before heading back into the TARDIS. The flashing began to quicken as the TARDIS began to vanish. The Time Masters figured out what was happening just as the TARDIS vanished. They began running but it was too late. The Vanishing point was then flooded with a green energy flash.

The Waveridder

Rory was standing in the cockpit of the ship, deep in thought. Hearing someone walk up beside him, he didn't need to turn around to figure out it was Amy.

"I know this must be strange for you," Amy said after a moment.

"I can deal with strange. I've been dealing with strange since The Doctor came into our lives. This is different," Rory sighed, feeling as old as those two thousand years he had spent guarding the Pandorica. "I have all these memories in my head. I know they're not mine but they feel so real. And I did…horrible things. People died because of me."

"It wasn't you Rory," Amy immediately protested and Rory laughed humorlessly.

"So The Doctor keeps telling me. But I still did them," Rory said haunted. "People are dead. I don't…I don't know who I am anymore."

"You are Rory Williams," Amy says firmly as she walked over and took his face in her hands, making him look at her. "A husband and a father. A nurse, a good man. You try to help people, even those you've only just met. You fell in love with a damaged girl who could never tell you how she felt until after she lost you and you still followed her into a time machine and waited two thousand years for her. You are a good man who had terrible things happen to him, but you are not a bad person. You are the love of my life and the best man I've ever known. The last six months have shown me that my life is only worth living if I have you to share it with."

"Amy…I'm such a mess right now," Rory said lowly.

"I was a mess for a long time. And you still stood by me, it's my turn now. It's called marriage," Amy told him, pulling him into a brief but sweet kiss. "We'll get through this, just like we always have."

Rory didn't think it was possible to fall more in love with Amy Pond, but she once again proved him wrong. As he marveled at the amazing woman that was his wife, The Doctor walked n.

"So, the Time Masters are taken care of, all we need to do is drop the so called Legends back in 2016 and then we can be on our way," The Doctor said.

"You're sure they can't come after us again?" Amy asked wearily, subconsciously wrapping her arm around Rory's.

"Positive. I fried all their technology. They can't get out of the Vanishing Point if they wanted to, they'll be too focused on trying to survive. Hopefully that'll give them some time to think. Now, come along Ponds!" The Doctor said cheerfully as he moved towards the exit.

"Wait, what about the ship?" Amy asked as she waved her arms around the ship.

"Oh, right, I'll take care of that," Rory said before looking up at the ceiling. "Gideon, wait five minutes than head into the sky. Initiate self-destruct sequence."

"Of course Captain Hunter," Gideon's voice said and Rory made a face.

"You sure you want to blow it up? This is quite something," River noted as she walked over.

"Only way to ensure it doesn't fall into the wrong hands. Besides, the less reminders I have, the better," Rory said darkly.

No one said anything, hardly being able to blame. So, they all exited the Waveridder. Outside, the Legends were all waiting as the group of four stepped off the ramp.

"So that's it then? We just go back to our lives?" Kendra inquired.

"It's not easy, but it can be done," The Doctor said as he looked over at Rory and Amy while thinking of Martha. "And I suppose that I'll be seeing you all again one day, although I can't guarantee I'll be wearing this face."

"Excuse me?" Stein asked confused.

"Oh, I don't always look the same. It's not weird," The Doctor shrugged.

"Kind of is," Amy noted and he looked at her betrayed as they all laughed a little at their antics.

"Okay, I just have one question," Sara said and they all looked at her. "What's with the bowtie?"

"Bowties are cool," The Doctor said defensively and all three Ponds rolled their eyes.

"Do not get him started on bowties," River told Sara, who merely nodded, still weirded out by River's resemblance to her mother.

At that moment, the Waveridder's ramp closed and they looked up as it began to fly into the sky. After it reached thirty feet in the air, it exploded in a blast of fire. The group stared at it for a moment before the fire faded from the night sky.

"Before we leave, I wanted to apologize to all of you," Rory said as he turned back to the Legends. "I know it wasn't actually me, but I still used you. People died because of me…Carter died because of me. I put you all at terrible risk and I wanted to say how sorry I am."

For a moment, they were all silent.

"I can't say I'll ever forget what happened," Kendra said, nearly choking as she remembered Carter dying. "But I know it wasn't your fault."

"Kendra's right, it was the Time Masters. You shouldn't blame yourself Ri – Rory," Ray corrected himself at the last minute.

"These Time Masters used you like a puppet. You wanna blame someone, place the blame where it belongs kid," Snart of all people told Rory.

"Can we go home now or what?" Mick grumbled.

London, 2012

Morning

After dropping the former Legends off in 2016, the TARDIS materialized in Amy and Rory's front yard. The doors open and Amy and Rory stepped out. Rory looked at the house with a hint of longing. He honestly didn't know how long it had been since he had laid eyes on it.

"Well, now that things are all sorted, we should be going," The Doctor said, gesturing to himself and River. "We'll be by in a few days, just to check in. Try and take a few days, settle back into things."

Amy and Rory could read between the lines. They were going to give them a few days to get reacquainted, so Rory could get himself sorted. So, rather than protesting, they exchanged hugs with The Doctor and kissed River on the cheek before watching as they headed into the TARDIS, which vanished soon after.

For a moment, they stood outside their house before Amy grabbed Rory's hand and led him over to the door. Unlocking it, she led him inside. Rory looked around, surprised by how clean it was. Too clean. Even when he'd lived here, it hadn't been this clean. The realization hit Rory like a lightning bolt.

"Have you not been staying here?" Rory asked in surprise.

"Not for the last four months, no," Amy admitted. "I couldn't stand staying here without you. So I moved back to your old place in Leadworth after The Doctor dropped me back off and waited for news."

"Amy…" Rory trailed off, seeing how much his absence had affected her.

"It doesn't matter now," Amy assured, placing a hand on the side of his face. "You're back now, that's what matters."

And so life went on for Rory and Amy. Rory went back to nursing and Amy found a job writing for a travel magazine. The Doctor and River would pop in to check on them every now and then. There would still be dark days, days when Rory woke up from nightmares, thinking he was still trapped by the Time Masters. Times when Rory would get a faraway look in his eye that Amy knew meant he was thinking of his time as Rip. But Amy had come to accept that she couldn't make those days go away, all she could do was remind him that she was here, allow their love to anchor him.

It wasn't always easy and Amy would forever hate the Time Masters for what they had done to her husband. But she couldn't change it. So she did what she always did: fought for the man she loved. And she would fight for Rory until the day she died.

So, the Time Masters were really just trying to screw with The Doctor, which is something I can easily see them doing.

The thing that bothers me about most 'Rip is Rory' fics is that most ignore one basic fact: Rip being Rory would destroy Rory's character because Rip is a pretty awful person. Even just the first two episodes show Rip is manipulative, self-serving and hypocritical. Rory being brainwashed is really the only way I can see the situation not destroying Rory's character.