So, this is actually based on the original series in the 80s. Not that I dislike the reboot, I just don't have a story for it. This story is set after the last episode of the old series. If you haven't seen it for a while, here are the characters that will be appearing from the old series (least so far), and a quick recap of where the series ended.

MacGyver-Obviously

Sam Malloy-His Son

Peter Thorton-MacGyver's mentor/boss and best friend

Murdoc-MacGyver's Arch-nemesis

If you need a recap on everyone's status by the last episode:

MacGyver met his son Sam for the first time (the mother and MacGyver had split up for work years ago, and then she never told him before her death. Sam only had a picture of the man his mother said was his father).

Macgyver helped steer Sam away from violence (he wanted revenge on the man who killed his mother) and then retired from the Phoenix Foundation to spend time with his new found son.

Pete stayed at the Phoenix Foundation, but wished them well.

Murdoc had been "killed" once again in an earlier episode, but, as always, they never found the body and MacGyver got a phone call with evil laughter, so...yeah...he's not dead.

Episode 1 Part 1: Ghosts

"MacGyver here. Pete! It's good to hear from you!"

Sam looked over the table towards his old man. He always got excited when his friend Pete called, but MacGyver wasn't smiling.

"I'm sorry Pete. Do they have any idea-yeah. Yeah. I'll be on the next flight out. Hang in there Pete." Macgyver hung up the phone and turned to Sam.

"What was that about. Is your friend okay?" asked Sam.

"Not exactly. Umm...you see, Pete had this niece a few years back, went missing, and, they may have just found her body."

"I'm sorry," said Sam. "You heading back for the funeral?"

"Well, it's a little more complicated than that."

"Wait, were you and she...?"

"Hmm, what, no! No. Nothing like that. It's...she was involved with dangerous people and...people Pete and I have had run-ins with before."

"So, when are you heading back?"

"Soon as possible, but look, I'm not coming out of retirement. I just need to help Pete. I'll wrap this up quick, and then we can get back to-"

"Dad," It still made Sam smile every time he said it, "Do you want me to come with? I am a pretty good investigative journalist. I can help you figure out what happened to Pete's niece."

Macgyver's face broke into an instant smile. "That would be great Sam." His smile faltered a bit. "But, I better feel you in more before you decide if you're coming or not. These people, this person she was involved with, was...the most deadly thing I've ever faced."

As the drove back to the hostel they were staying at, MacGyver gave Sam a quick overview of Murdoc and the many times he had tried to kill MacGyver and/or Pete, and that, while listed as dead, his body had never been found.

"I learned a long time ago that trusting Murdoc was gone is a fatal mistake," said MacGyver.

"Fair enough, but you still haven't told me how Pete's niece got involved."

"Well, that story actually started before I met Peter Thorton. Back when he worked for the DXS and was first tracking Murdoc. See, Pete's niece, Jenny, had always been a bit of a wild card. Her parents had died when she was young and she'd taken it badly. Pete tried to keep an eye on her, but...it wasn't the same."

Sam nodded sadly. "I can imagine what she was going through."

MacGyver smiled at him sadly. "Yeah. Well, Jenny eventually started to straighten her life out, and Pete wasn't as worried about her. Pete had almost caught Murdoc in Lisbon, but just missed him. When he got back to the states, Jenny called him and asked him to meet up. Wanted to introduce him to her boyfriend."

"Oh no" said Sam. "It wasn't...?"

"Oh yes it was. Pete walked into the restaurant and her boyfriend "Mark" opened fire. It was pure luck that Pete got himself and Jenny out of there safely. It messed Jenny up for a while, but, with a good therapist and a lot of support from Pete, she got herself pulled back together."

MacGyver zipped up his duffle and sat down on the bed.

"So, what happened next? Based on what you've told me so far, I assume that wasn't the end?"

"No, no it wasn't. A few years later, Murdoc turned back up in Jenny's life."

"Uncle Pete, please, listen to me. He wants to come in. He wants to turn himself in."

"Jenny, what are you thinking! This is the man who lied to you to try to kill me! Tried to kill me multiple times I might add! Now, where are you? You need to get away from him!"

"Look, just meet us at the redwood forest tomorrow. Right at the trailhead of Mom's favorite hike. He'll have no weapons. He only asks that you bring a small group. 4 or 5 men that you trust. He says his employers are desperate to stop him, and he's sure they've turned a couple of your people."

"Jenny, you're not safe with him!"

"Please Uncle Pete. I...I know what he's done. But, I've seen another side of him. A side you never saw. He wants to change. Please! Just give him a chance. I've got to go now. I'll see you tomorrow. 3 pm. I love you Uncle Pete."

"Jennifer, don't hang up! Jenny!"

Pete slammed the reciever down.

MacGyver looked at Pete in shock. "What's she thinking Pete? She was there when he tried to kill you.

"I don't know MacGver. He's probably spun her some tragic story. He was always good at creating aliases. All I know is that my sister would be rolling in her grave. We've got to go Mac. We've got to get her away from him."

"Of course, but we need a plan. I don't believe for a second that Murdoc is going to try to turn himself in."

"Yeah, I'll get a team together. Just...be...ready for anything MacGyver. We may need to improvise."

Macgyver patted Pete on the shoulder. "When has that ever been a problem?"

They got to the meeting spot 2 hours early. Peter Thorton had 10 men surrounding the area, but only 3 other men in plain view near him and MacGyver. He'd taken Murdoc's advice and chosen 3 men he trusted. Men who had just as much reason as him to want to see Murdoc behind bars.

Right at 3 pm, a jeep started to pull up to the spot. Stopping 4 yards back, Jenny stepped out, with Murdoc close behind, holding her arm.

"Uncle Pete?"

"Jenny! Are you okay?"

"Of course I am!"

"Yes, Peter," called Murdoc. "She's as safe as can be. You know I would never harm Jenny. I want to come in. This life of a paid assassin is wearing. I need a fresh start."

Jenny turned back to Murdoc and gave him a huge smile.

"Alright." called out Peter. "Come closer, but stop when I tell you."

Murdoc and Jenny moved towards them. Murdoc kept Jenny in front of him. His eyes darting back and forth looking at the tree line. 2 yards away, Pete stopped them.

"That's far enough. Jenny, you come here."

Jenny shook her head. "No, I'm staying with him. You can't just shoot him."

"Jenny, I'm not going to shoot him."

Jenny shook her head. Murdoc smiled. He held his arms wide. "I'm unarmed Peter. As promised. You can ask Jenny if you don't believe me. She saw me dress this morning." Jenny blushed violently, but gave a small smile and nod.

Peter gripped his gun tighter.

"Pete, relax," said MacGyver, stepping forward.

"Jenny, we have to search him. Just step a few inches to the side. If he's telling the truth, no one is going to hurt him. I promise."

"Ah, MacGyver, the voice of reason, as always. Don't worry my dear. Your uncle may be trigger happy, but dear MacGyver here I trust. Remember, your Uncles friend doesn't like guns. Just swiss army knives."

Jenny looked to Murdoc worriedly, but stepped to the side.

Murdoc held out his arms again and one of the men started to frisk him. He was wearing a Kevlar vest, but it was quickly removed.

"Little unusual for you Murdoc," said MacGyver.

"Oh, it never hurts to be careful MacGyver."

"He's clean." said the soldier.

Murdoc smiled. "As I promised. So, what now Pete?"

Pete held out a pair of handcuffs. "Cuff yourself and we'll all be on our way."

Murdoc shrugged and took the cuffs. "Jenny, will you do the honors?"

Jenny took a step toward Murdoc, but Pete put out his arm to block her. "You cuff yourself Murdoc."

Murdoc shrugged again. But as he lowered his head to put the cuff on, MacGyver felt a movement behind him. It all happened in one big blur. One of the men stepped forward, bring his weapon up to fire. Jenny saw the movement and pushed past Pete, rushing forward to protect Murdoc. The minute she reached him Murdoc grabbed her and reached behind her. Jenny had been wearing a Kevlar vest too, but it looked like Murdoc had stashed something inside it. Out slipped a slender pistol, flatter than any MacGyver had ever seen before. The soldier fired, hitting Jenny in the chest, and pushing her and Murdoc back towards the edge of the road. Murdoc fired, hitting the soldier. He aimed his gun at Pete.

"No!" cried Jenny. She tried to grab the gun, but all she did was push Murdoc and her over the edge of the hill the road rested on, sending them tumbling down the hill. They heard the gun go off.

Pete ran to the edge with MacGyver right by him. "Jenny?!"

"She's alive Peter Thorton! I told you to choose some trustworthy men. Next time, try to take my advice."

"Murdoc, if you hurt her I swear I'll..."

"Here's how it goes Peter. I'll be sending you a message later today with a new meeting place. Come alone and trade yourself for Jenny, or she'll be dead by morning. Understand? Try to follow us, and she'll be dead too. Then you can bury her next to your sister!"

"So, he never meant to turn himself in?" asked Sam

"No. Best we can figure it, his plan was to get close, keep Jenny near him, and pull the gun at the right moment. We didn't even think of searching her. I doubt she knew he'd hidden the gun on her. The soldier that tried to shoot him was a surprise to all of us. He'd lost his wife in a car bomb Murdoc had placed at a DXS safe house. Pete hadn't realized that he wanted to personally punish Murdoc for it. He thought he just wanted to see him in prison like the rest of us."

"So, what happened at the meet?"

"It never took place. By the time we got down the hill, Murdoc and Jenny had disappeared. Murdoc never sent a message. Never set a place or time to meet. We never heard any news of Jenny again. We'd always assumed that...I don't know...she'd tried to fight back, or escape, or something, and gotten killed."

"And they only just found her body?"

"They think they might have found her body. If it is, she only died recently. It raises even more questions. That's why Pete's asked me to come in. It could mean that Murdoc is really out there, and perhaps active again. If that's the case, are you sure you want to come?"

Sam thought for a moment, but then nodded. "You helped me catch the man who killed Mom. We put him away. Sounds like this Murdoc is an even bigger nightmare. I want to help you put him away. Besides, who else will watch your back?"

MacGyver smiled. "Alright. We better get going then. But, hey, listen Sam, we really do need to be careful. With Murdoc, always expect the unexpected."

A car met them at the airport with Peter.

"Pete" said MacGyver, walking up and giving him a hug.

"It's good to have you back Mac," said Pete.

Sam smiled. He hadn't known Pete Thorton before he lost his sight, but his Dad had told him a lot of stories. Pete and his Dad had saved each others backs many times. He hoped he could watch out for his Dad as well as Pete had. Especially if this lunatic Murdoc was gunning for them again.

"So, on the phone, you said they weren't sure if it was her?" said MacGyver as they drove to the Phoenix Foundation.

Pete looked down. They found a woman's body in the river. She...she had a tattoo on her left shoulder. A celtic band like Jenny had. But...but the body didn't have a head."

Sam swallowed hard. He felt sick.

"They're taking a DNA sample from the body. The specialist will be arriving any moment. We don't have an old sample from Jenny, but we're going to test it against my DNA. It'll tell us if the woman we found is a relation. If it is...Jenny."

"You don't have a specialist in house?" asked Sam.

"It's a fairly new process," replied Pete.

Macgyver nodded. "Any other leads?"

Pete shook his head. "Not yet. Nothing was found on or near the body."

"Mr Thorton?" said a young guard walking up.

"Yes?"

"There's a woman who showed up shortly after you left. She's asked to speak with you. She won't tell us what about."

"Tell her I can't see her today."

"We did sir. We know you're busy, but she insisted she had to see you today. She's just in this room over here."

Pete sighed.

"Want us to come with you?" asked MacGyver.

Pete smiled. "Just like old times MacGyver."

They walked into the conference room. A young woman with dark brown hair stood up. She looked about Sam's age, with piercing blue eyes and an aquiline nose.

"Hello ma'am," said Pete. "How can I help you?"

"Are you Peter Thorton?"

"Yes."

"I'm sorry, I...I wanted to speak with you alone."

"Oh, this is my assosciate MacGyver and his son…"

"MacGyver? Oh, that's alright then. Mom said I could trust him too."

"I'm sorry," said Pete. "Who are you?"

The young woman took a deep gulp. "My name is Clarissa Johnson. I'm Jenny Johnson's daughter."

A few hours later, Sam shook his head. Well, no one could ever say his Dad's friends were boring. Clarissa had shown them her ID. Pete had been skeptical at first, but she'd known a lot of facts about Jenny. She'd even agreed to a DNA test. When the specialist had arrived, they ran two tests. The body was identified as Jenny, and Clarissa was her daughter. Clarissa had asked if she could see her Mom's body. MacGyver had tried to discourage her, but she had insisted. Sam was now waiting with Pete. Pete was just sitting there. Sam couldn't tell if he was grieving or just in shock.

"Are you okay Mr. Thorton?" he asked?

"I have a great niece. I mean, I was young when Jenny was born, but still. I'm old enough to have a great niece." Pete just kept looking down. "I guess I know how MacGyver felt when you found him. He found out that he had you and lost your mother all in the same day."

Sam grimaced. "I'm sorry about Jenny. I was hoping it would turn out to not be here."

Pete shook his head. "The minute Clarissa showed up, I knew it would be. For her to be looking for her mother right when we found a body was too big a coincidence."

MacGyver walked with Clarissa into the morgue.

"Where did they find her again?" asked Clarissa, teary eyed.

"In the river. I'm sorry." Clarissa nodded. She stepped through the doors and walked up to the table. She stared at the body under the sheet.

"You, you said she went missing a week ago?" asked MacGyver.

Clarissa shrugged. "I got worried a week ago. She usually calls me every day to check in. Missing a day here and there isn't unusual, but it had been a few days, and I was worried."

"How did you know to come here?" asked MacGyver.

"Mom always said that if anything happened, I should find Uncle Pete. He would help us. I just...I just never thought that..." Clarissa pulled back the sheet and shivered. She turned quickly into MacGyver's arms.

MacGyver wrapped his arms around her, holding her tight as she sobbed.

"It's okay. It's okay. Let it out."

Sam looked up as MacGyver and Clarissa came back in the room. Pete looked up at the sound of their footsteps.

"We need to talk," he said gently.

MacGyver helped Clarissa into a chair. He raised his eyebrows at Sam sitting by the fridge. Sam hurried and grabbed a cola from the cooler to hand her. Clarissa smiled at him when he handed it over.

"So," said Pete. "You and your mother had been on the run?"

Clarissa shook her head. "More in hiding I'd say. I never really felt the effects of it, except once. For the first 10 years of my life or so, I lived with a family, here in the states. Mom would come and visit now and then. Then, one day, she showed up all of a sudden and took me away. She looked banged up and frightened. After that she put me in a boarding school in France. She would come and see me around the holidays or my birthday. That's when she first told me about you Uncle Pete...I mean...Mr. Thorton."

"No, to you I'm Uncle Pete."

Clarissa smiled. "She said we needed to hide from some dangerous people, but that if anything ever went wrong, to come and find you here. She told me about you too MacGyver, but, I didn't know about..."

"Sam. Sam Malloy."

Pete looked over towards MacGyver's general direction, a questioning look on his face. MacGyver nodded.

"Clarissa-"

"Please, my friends call me Riss."

"Riss. Did your mother ever talk about your father?"

Riss shook her head. "No, not really. I always got the impression her feelings for him were very complicated. I mean, she loved me, she was my Mom. I just, the way she looked at me now and then. I could tell it was painful for her to be around me."

"Families can be complicated like that," replied MacGyver.

"Look, I know I don't work for you here, but, if there is anyway I can help. I've been studying forensic science in Germany, and, if there is any way I can help. I want to find the people who did this to my Mom. I want some answers."

"We'll see what we can arrange," said Pete. "For now, do you have a place to stay?"

"I just got into town today, I'll find a hotel..."

"Nonsense," said Pete. "You'll stay with me. In fact, I want all of you to stay with me until we figure out who is behind this."

Riss nodded. "Do you have any leads? Do you know who was after my Mother?"

Pete hesitated. MacGyver looked down. It was Sam who spoke first.

"From what they've been telling me, there's an assassin named Murdoc who has been targeting your uncle and my Dad for a long time. Your mother got mixed up in it years ago. We don't know if he's the one she was hiding from, but their last run in, would have been around the time your Mom took you to France."

MacGyver gave Sam a warning look, but Sam ignored it. He knew what it was like to only be half sure where you came from. To feel alone in a world you barely trusted.

Riss looked at Sam. "So, what do we know about this Murdoc?"

The next day, MacGyver and Pete went to look through any recent assassinations to try to see if any of them could be Murdoc. Sam and Riss started investigating the body. Riss was working with the forensic specialists from Phoenix, but MacGyver had wanted Sam to keep an eye on her.

"So," said Riss while they worked. "If the gossip I've been picking up is to be believed, you're the reason MacGyver left working for the Phoenix foundation?"

"Oh, someone tell you the whole sob story."

"Just that you two met a year ago and became close really quickly. That's really special Sam. I always wished I'd known my father."

"It was surreal meeting him. I'd had his picture along with my Mom's for so many years. Just, ran into him by accident."

"You didn't come looking for him?"

"No, I...I was...I was looking for the man who killed my Mother."

Riss paused, and looked up from her work. "I'm sorry. I didn't know. I'm sorry."

Sam shook his head. "No don't be."

Finally, Riss broke the awkward silence.

"Does, does it get easier?"

Sam nodded. "A bit."

"When you caught the man?"

"I thought it would. Really though, it wasn't finding him, it was finding Dad-MacGyver. Finding a new purpose I suppose."

"But you did find the man who killed your Mother?"

Sam nodded.

"I hope you made him pay. I want this bastard to pay."

"Look," said Sam, "I want to nail this guy too. You deserve that. But, you're going to need something beyond that. I got so consumed with revenge at one point, I almost got my Dad killed. He's the one who pulled me out of the pit, metaphorically and literally actually. Helped me realize that justice and revenge weren't the same thing."

Riss gave Sam a confused look. "I don't know if I quite get what you mean?"

"It took me a while to get it too."

"Well, what do I have to look for after this. They won't say anything, but I get the feeling Uncle Pete and MacGyver know more about who my mystery Dad could be than they are letting on, and it doesn't look like a happy ending for me. What do I have left other than finding Mom's killer?"

"You have your Uncle Pete. I know that finding you, means the world to him."

Riss smiled sadly. "He's almost a perfect stranger to me."

"So was my Dad when I met him. But, I knew he cared. Even when I didn't want to admit it. Even when I messed up."

Riss looked uncomfortable. "I just can't think that far ahead right now."

"Sorry," said Sam, turning away.

Riss shrugged it off. "Could you hand me that other sample over there?"

Sam picked up a slide and handed it to Riss at the microscope. "Find anything?"

"No, the...the cuts were a blade, but...there was too much...erosion to tell what kind. And, we're not finding any traces of the weapon in these samples. Or anything to indicate where she was before he dumped her in the river."

"So you think it was Murdoc?"

Riss gulped. "I don't know what I think anymore."

Sam looked back at the items found with Jenny. "Hmmm...you know, there is one really weird thing here."

"What?" asked Riss.

"Did you notice how few stains there are on the dress collar? Wouldn't there have been more?"

Riss thought for a moment. Her brow darkening. "Not if she was...if she was upside down when it..."

Sam gently touched the dress. "But there are stains on the inside of the collar. Just not on the outside."

Riss furrowed her brow. "Let me look at that." She examined the dress. "It is odd. Let me make a note of this for when the rest of the lab technicians get back. Something is really off with this." She wrote some notes down on a pad.

"Um...Sam...I kind of need a break. I just need some fresh air, but, I don't really want to be alone if..."

"No, I could use a break too." Together they walked out around the building.

"So," said Sam outside. "What was it like growing up in Europe." Riss smiled. "A little boring at first. I was at a boarding school remember. What about you, what was your life like?"

"A little hectic. I'd have killed for some boring as a kid."

Riss rolled her eyes. "Oh come on, it can't have all been bad."

Sam smiled. "Not when I was older. I hate staying in one place too long."

"That I can understand," said Riss. She smiled at Sam and took his hand in hers as they walked.

Meanwhile, MacGyver and Pete had chased down multiple leads all day, but always at a dead end. There had been plenty of assassinations over the year, but no factors to clearly point them out as Murdoc's handiwork.

"Maybe we're going about this the wrong way Pete. Instead of looking for leads on Murdoc, we should look more closely into Clarissa's childhood. Maybe the school has mailing addresses from Jenny. We both know who she was running from."

Pete shook his head. "I just don't get it MacGyver. If she got away from him, why didn't she come to me?"

MacGyver grimaced. "We can both guess why. Her age...It's a pretty safe bet about who Clarissa's father is."

Pete frowned. "There is nothing safe about Murdoc. I'm not saying I love the idea, or that I would have loved it, but I would have protected both Jenny and Clarissa if they'd come to me."

"I know Pete, and deep down Jenny knew that too. She just felt ashamed. She fell for Murdoc twice, and she probably felt like she'd let you down."

"I know I just...aghh! Can we ever get clear of his ghost?!"

"We're gonna try. For now let's head back and get some more information from Clarissa about the school she was at."

It was dark when they all got back to the HQ. Sam could tell that Riss was still weighed down, so he'd shown her around L.A. As they walked back up the steps, Riss was laughing.

"Thanks for showing me around Sam. I needed that today."

Sam smiled. "It was good for me too. Maybe some day you'll show me around France or Germany."

"Maybe," said Riss. "I think I'd like to start somewhere fresh some day though. Somewhere I've never been."

"Well, make sure you send me your address when you do".

Riss smiled at Sam. She stopped walking. Sam stopped next to her. She stepped closer to him. Sam leaned in. Before he knew it, they were kissing. She was a good kisser. Just the right amount of pressure. Just the right force. She smelled amazing. Like lavender and lemon. Just then Sam heard a cough behind him. Breaking apart, he saw MacGyver leading Pete into the doors.

Pete motioned towards them. "Was that what it sounded like?" Riss looked down, blushing.

"We'll talk about it inside," said MacGyver.

Sam looked worried, but when he glanced at Riss and saw her smile, he couldn't keep a goofy grin from creeping up his face too.

Inside Pete headed down the hall to grab some things before they headed home.

MacGyver turned towards Sam and Riss.

"Oh, hey, Riss," said Sam. "Should we see if they have any feedback on the strange stains?"

"Oh, yeah, I'll go check."

"I can come too?" offered Sam.

"Sure-"

"Nah," said MacGyver. "You run ahead and get the info. I'll be right here with Sam."

Riss gave Sam a look that said "Sorry, but better you than me" and hurried off.

"So," said MacGyver.

"You know, those stains could be really important. We really should go see what it is about," offered Sam.

"Oh, I'll go check in a moment. But, before I do, we're going to have a little chat."

"Dad, you may forget, but I am an adult. I have been around girls before. Clarissa is an adult too."

"And she's Pete's niece and in a vulnerable state."

"Hey, she kissed me!"

"Sam, I'm not upset. I just want you to be careful. Alright? I've been there. It's really easy to get your emotions all mixed up in a scenario like this, and not thinking straight while you do it is not going to do her or you any favors."

"And I appreciate that. But, I also think you need to trust me. I'm not going to do something stupid."

"So that kiss was a thought out plan?"

"That kiss, which is not exactly your business, came at the end of a day spent...together. We've actually got a lot in common. In more ways than one."

MacGyver noticed the offensive tone in Sam's voice. "I'm sorry. I hadn't thought how hard a case like this would be on you."

"It's not." MacGyver looked Sam in the eyes. "But it is a lot. I'm fine Dad. Really."

"Alright," said MacGyver. "But I'm here if you need to talk."

Just then, all the lights in the building went off.

"Is it supposed to do that?" asked Sam.

"No, it's not," said MacGyver. Sam started forward.

"No, you stay here and wait for Pete." said MacGyver. "I'll go get Clarissa."

"Kay. Be careful."

"You too."

MacGyver walked down the halls and around the corners. He found a lamp and took it's bulb and some wires to make a quick flashlight. There was no power from the socket, but there was a battery in a radio on the table.

He could hear voices throughout the building. The lights shouldn't have been shut off till everyone was out. Just as he reached the hallway with the lab, he heard glass breaking and shouts from behind him. Running, he hurried into the lab.

"Clarissa are you here?!" called MacGyver

"Yes, yes, I'm here!" She said running forward. "What's happening?"

"I'm not sure, but stay close," MacGyver turned back towards the door, but heard a chilling click behind him. He turned to see Clarissa holding a gun and pointing it at him.

"I'm sorry," she said flatly. And then something hit him from behind, and everything went dark.