Okay, here's the second part. Maybe it will explain Sam a little bit more, but then again, maybe it won't.

I have added an idea as to how Sam got his information, something that wasn't in the show but could have easily been a part of Sam getting to know MacGyver and Pete.
I'm still practicing with these stories. As I've said before, I view them as writing exercises, and I really do appreciate your constructive criticism, because it helps me figure out where I need to improve for the next story. That is really the only way to strengthen as a writer--feedback. So, thank you!
Oh--and enjoy!
A Crack in the Foundation Part Two
Rated: PG
MacGyver ran out of Pete’s office and quickly descended to the first floor lobby of
the building where he stopped at the front security desk. He described Sam perfectly to the guard on duty.
“Well Frank, have you seen him?” He asked, panting from running.
“Yes, he just came by here a minute ago,” Frank said.
“Do you know which direction he was headed?”
“I think he was headed toward the parking garage. I can review the security tapes and see…”
“No Frank, that’s fine,” MacGyver said. “I don’t have time. Thanks.”
MacGyver took off running again, hoping it wasn’t too late to catch up with Sam. The parking garage was one more level below the main floor lobby, so he got in the elevator and descended another floor, waiting impatiently. Fortunately, he knew what level of the garage Sam would exit from, since they had both taken their motorcycles and parked near each other. When he stepped out into the garage, he heard the engine on Sam’s motorcycle start up and he crouched behind a nearby vehicle so that he wouldn’t be spotted. He watched until Sam was clear of the garage and jumped onto his motorcycle, hoping that busy midday city traffic would slow down Sam’s progress and he could catch up with him.
As he cleared the cool darkness of the garage and entered the brightness of the day, he saw Sam racing down the street at a fast speed, but not fast enough that he couldn’t follow him. Both of them had to contend with traffic obstacles, which kept Sam from completely leaving his line of sight. He weaved in and out of cars, and MacGyver did the same, trying to maintain a good distance so that Sam wouldn’t know he was being tracked. Sam was good at trying to evade him, but he was just as good at keeping up with him. As he continued to pursue Sam, thoughts raced through MacGyver’s mind about the new information he’d learned about the young man. He had started as a relative stranger, and just when he thought he could be confident in knowing who he was, he had changed again into something MacGyver dreaded. The whole situation overwhelmed him until he wasn’t sure what to believe anymore.
A massive semi-truck crossed the intersection they came to, and Sam darted out in front of it, barely missing catching the front end of it. The driver of the truck honked loudly, and MacGyver looked ahead, waiting until the truck passed to see how far Sam had progressed. When the truck cleared, he didn’t see him anywhere. Still, MacGyver decided to press on, clearing the intersection and continuing down the street. He saw no sign of Sam anywhere. He back-tracked and retraced where Sam might have gone, driving down alleyways and side streets, but he knew it was hopeless. Sam was out of his range, and he had no clue as to where he might have gone. There was simply no trail to follow.
***
The abandoned warehouse’s dilapidated exterior cleverly disguised the sophisticated technological base of operations for Joseph Gorman, a former East German Stasi agent. He watched as his young operative entered the warehouse on his motorcycle, cracking his knuckles beneath his leather gloves anxiously. Ever since the Berlin Wall fell, life had not treated him well. His bitterness and years of struggle had aged him, weathered his features. He also had a missing index finger as a result of all his years in covert operations, cooperating along with the Soviets. A mission gone wrong and months of torture as punishment for his failure had left him missing the finger. In its place was a carefully crafted silver finger that matched the size and length of his original, but not even a skillfully created replacement could make him forget what happened, and who caused it to happen.
“You’re late,” Gorman said in his thick German accent, watching Sam dismount from his motorcycle.
He waved away several of his men, raising his gloved hand in a signal that they had come to interpret as meaning that he wished to be left in complete privacy. He waited until they were out of the room to continue, watching them leave with calm yet severe gray eyes.
“I’m sorry,” Sam said, removing his helmet and approaching Gorman.
Gorman frowned, noticing the concerned expression on Sam’s face. “Something went wrong,” he said.
“Well…yeah, it did,” Sam said. “They know about me. They know I’m a fraud.”
Gorman’s posture stiffened. “What else do they know?” He asked.
“They know I’ve been stealing their intelligence, but they don’t know who I’m giving it to.”
Gorman glared at him with his piercing eyes, looking as if he was prepared to strike him, his rage boiling.
“I don’t know how this happened,” Sam said. “I’m truly sorry.”
Gorman’s hard features softened. “It is all right,” he said.
Sam looked at him in surprise. “All right?” He asked. “How could it be all right when…”
“I want you to go back to them, especially to this MacGyver,” Gorman said, spitting out his name in disgust. “You will be honest with him, admit to what you have been doing.”
“But…”
“It will still work with my plan. In fact, it might actually work to our advantage much better than I thought.”
***
“He’s gone Pete, I lost him,” MacGyver said, flopping onto Pete’s sofa in his office. “I have no idea where he went, either.” He picked up the file created on Sam and examined it again. “Are you sure your boys working on this thing haven’t come up with any new clues about who he’s been leaking this information to?”
“I’m afraid not, Mac,” Pete said. “Once we established a background and profile on him, we learned what he had been doing, but as to whom he might be giving the information to, well…we’re still working on it.”
“Great,” MacGyver said.
He continued to read the file repeatedly, unable to put it down, its contents preoccupying his thoughts. He focused particularly on the DNA results, shaking his head as he read them, still not fully able to believe it. Sam had given him some convincing arguments as to why he was his son, and he had taken it on good faith that he was. At the time, he didn’t think he needed a DNA test to prove it, but in hindsight he supposed he should have requested one. He relied upon results and science to prove things, and in this case he hadn’t, much to his detriment and the detriment of The Phoenix Foundation. He looked up at Pete, trying to do anything to get his mind off the file, even though he was still drawn to it.
“Pete, is there any way these test results could be wrong?” He asked.
“I don’t think so, Mac,” Pete said, shaking his head gravely. “The sample came directly from Sam, and we’ve had it checked and looked at by our lab scientists several times to ensure accuracy. It matches with who it says he is in that file, not to you. I’m sorry.”
“Could you check the results again just to make sure?”
“I don’t see how the results would change, but if it comforts you, I’ll have my experts in Genetics and DNA look it over again.”
“I appreciate that, Pete.”
“You’re really worried, aren’t you?”
“Yes, I am, Pete. If Sam isn’t who he said he was, and if he’s selling our secrets to our enemies, then it’s serious. If he turns out to be my son, then he might be innocent. That’s why I want you to make sure.”
Pete nodded. “I understand, Mac,” he said. “I’ll have them work on it right away. Meanwhile, why don’t you go home to your loft and rest? I’ll call you when I have more information, okay?”
“All right, Pete.”
***
MacGyver almost had to perform an act of pure stealth to enter his loft without attracting the attention of his nosy neighbors. They meant well, like Mama Lorraine, but he felt they took the spirit of community a little too far. He knew that if they found out he was back, they’d spontaneously arrange some kind of block party in his honor. While he knew they cared about him and were just being friendly and warmth, tolerance, and inclusion was a part of their nature, sometimes, especially now, he just wanted to be left alone. Pete had taken care of the place while he was gone, and he was relieved to find everything still in order, just the way he left it. There weren’t any new graffiti artists looking to decorate his wall, and there weren’t any empty cartons of food sitting out on the counter. All he was confronted with was the peace and seclusion he needed after discovering this new information regarding the young man who claimed to be his son. The phone rang just as he was about to settle down on his sofa. He answered it, and it was Pete.
“I just received an update on the DNA test results,” he said.
“Really? Man, they’re fast,” MacGyver said. “So, what does it say?”
“It’s still the same, Mac. Nothing’s changed.”
MacGyver sighed. “Test it again, Pete,” he said.
“What? But MacGyver, these results are conclusive!”
“I know, but I want them looked at one more time.”
“That’s what you said before,” Pete said. “Pretty soon, you’ll want test after test…Mac, when is it going to end? I’m sorry it turned out this way, but sooner or later you’re going to have to accept the results. Sam isn’t legitimate.”
There was a pause on the line.
“MacGyver, are you okay?” Pete asked. “Would you like me to come over there? Look, I know this is hard…”
“No, I’m fine, Pete,” MacGyver said. “Maybe you’re right. Maybe the lab staff is right. Still, I want another check. Just one more. Please, Pete. I promise this will be the last time.”
“If it will make you feel better…sure, I’ll do it.”
“Thanks, Pete.”
“You get some rest, okay? I’ll let you know what else I find.”
“Goodbye, Pete.”
“Take care of yourself, friend.”
When MacGyver hung up the phone, he thought about Pete. He was his closest friend. Of course he was looking out for him and had his best interests in mind. If that included telling him that his son was a fake, then he felt it was his duty to tell him, as difficult as the news was. Still, MacGyver wanted to hold out hope that something somewhere went wrong. He was just getting used to the idea of being a father, and now it had been ripped away from him so quickly that he could barely process it. The doorknob to his front door began to jiggle, and MacGyver ducked behind his sofa, realizing that he hadn’t bolted the door. He waited to see who was coming in, expecting Mama Lorraine or any number of people from the neighborhood. Instead, as he peered around the edge of his sofa, he saw Sam. He debated whether to surprise him or not, but he decided just to stand and show himself.
“I must admit you really had me going,” he said.
Startled, Sam stopped and looked at him, his eyes wide.
MacGyver approached him calmly, his anger visible in his blazing dark eyes. “Where did you get the locket? Did you steal it, or did one of your fellow conspirators get it for you? Or do you have any other proof that you’re my son? A birth certificate perhaps?”
“MacGyver,” Sam said, backing away from him, afraid he was going to get hit. “It’s true. I knew you found out that I’m not your son.”
“So, you’re not?”
“I’m not, MacGyver.”
The words coming from the young man who had posed as his son stung MacGyver more than the damning evidence from the DNA test results. No longer was he calling him “Dad.” He was using his name as if he were any other friend or acquaintance, not a blood relative, not his son. He stood there, inches away from Sam, unsure what to do or say next.
“If you’ll just listen to me, I’m sure we can straighten this out,” Sam said, still watching MacGyver carefully to make sure he wouldn’t get punched.
“You lied to me,” MacGyver said. “You stole valuable classified information and passed it on to God knows who! Why should I listen to you now?”
Sam nodded. “I know what I did was wrong,” he said. “I came here to explain. If you’ll let me do that, then you can hand me over to the authorities and I promise you that I’ll tell them everything I know. But please, MacGyver, I have to talk to you alone first. Do we have a deal?”
MacGyver sighed loudly. He backed away from Sam slightly, indicating his openness to hearing what he had to say. “Go ahead, tell me,” he said. “I’ll listen.”
“I appreciate it,” Sam said.
“So, tell me…why? Why me?”
Sam licked his lips and stared at the floor. “I was…hired to shadow you while on assignment,” he said. “I had to learn how you worked and where you worked. The people I worked for thought it would be easier to gain your trust if I told you I was your son. It was the perfect cover. I had some resemblance to you, and my employers managed to find Kate Malloy’s locket through their contacts in China. They knew all about you and your relationship with her. They could have chosen any of your past relationships, but they chose Kate because she had been working in China, and you were on assignment to expose Chinese labor camps. It just made perfect sense. They knew who you were and where you worked, but they just needed someone from the outside close enough to you that they could infiltrate your organization through my espionage. Once I gained access to you and The Phoenix Foundation, I was able to steal what I needed to. I learned about your computer systems, scouting them out that day you showed me the Foundation and I told you I had to use the bathroom. You had introduced me to everyone as your son, so they had no problems answering a few innocent questions about the computers. I just went from there. I’m sorry, MacGyver.”
MacGyver looked down at his photo album, now closed on his coffee table. “So, you’re sorry…for what? Using me, or for stealing our information?” He asked.
“Both, I guess,” Sam said. “Look MacGyver, I know nothing can make this right again, but I came here to do what I could, to tell you the truth.”
MacGyver sat on his sofa and leaned forward, his elbows on his knees. He cupped his face in his hands and sighed. “Why did you do it, Sam?” He asked. “You were a photojournalist. Why did you turn to spying on our government? Was it for money? Power?”
“No,” Sam said. “Actually, it was because I wanted more adventure in my life. When I learned about you, I admired you. I wanted to do the same things you did.”
“Yeah, well I never sold out my country,” MacGyver said, turning to glare at him. “That’s the major difference between you and me.”
“I know,” Sam said, sitting across from MacGyver, the coffee table with the closed photo album separating them. “I was stupid and impulsive. That’s why I came here. To apologize and let you know that I’m tired of hiding, tired of running. I want to turn myself in and help you, MacGyver, kind of as one last gesture of goodwill I guess.”
MacGyver studied Sam’s eyes and his facial expressions. He looked sincere. Strangely, he looked a lot like him. Some doubt still lingered in his mind. He wondered if there might still be a chance this young man was actually his son.
“Sam,” he said, “if someone made you do this, it’s okay. You can tell me who it is, and I’ll go after him.”
Sam cocked his head to the side and frowned. “What are you talking about?” He asked. “You still think I’m your son, don’t you?”
“It’s just very difficult for me to accept it.”
Sam laughed slightly, incredulous. “Before, it was difficult for you to accept the possibility that I might be your son,” he said.
“I know, but I…”
Sam looked directly at MacGyver. “MacGyver,” he said firmly. “I am not your son. No one made me spy on my country. It was my decision. A foolish one to be sure, but it was my choice to make. I know you grew to like me. I did, too.”
“Is that why you spent so much time with me? After I left the Foundation, I couldn’t have been any use to you. You could’ve killed me if you wanted to after you got what you wanted from me.”
“Yeah, well I’m not that kind of person. I may be a traitor, MacGyver, but I’m not a murderer.” He studied MacGyver. “Actually, I thought I could get away from this whole business, so I left with you. I didn’t realize what a mess I created, and how I’d have to tell you, but that’s why I came back. I had to tell you, and I have to try to correct this situation and help you.”
MacGyver arched an eyebrow. “You really want to help?” He asked.
“Yes.”
“How do I know you’re not just playing some other game with me?”
“If I was, I wouldn’t have been so honest about my deception.”
MacGyver nodded. He stared at the closed photo album again, thinking momentarily about Kate Malloy. “If you want to help straighten this out, you’re gonna have to be questioned and agree to be prosecuted for your crimes,” he said. “Perhaps with your cooperation, you can get a reduced sentence…but Sam, you’re going to have to answer for what you did. Do you understand?”
“Of course.”
MacGyver looked up at Sam. “Is that a deal?” He asked.
“MacGyver, I have no problem with this,” Sam said. “My conscience has been bothering me, and ever since I got to know you…well, I know I’m doing the right thing.”
Once again, MacGyver studied Sam, and decided he looked sincere. “Good,” he said. “The first thing you can do is tell me the names of who you’ve been working for…”
Suddenly, several men burst through the door. An older man wearing black leather gloves grabbed Sam and pointed a gun to his head.
“No!” Sam shouted, struggling.
“Take it easy, Sam,” MacGyver said. “Don’t provoke them.” He looked at the man holding Sam, thinking he looked vaguely familiar. “Who are you? What do you want?”
Gorman smiled and laughed. “All those questions will be answered in due time, MacGyver,” he said.
MacGyver squinted at him, trying to place him. “Do I know you?” He asked.
Gorman smirked. Briefly, he felt the phantom pain of his missing finger. It seemed to increase any time he looked at the man he despised. “Not directly,” he said, “but you’ll soon learn who I am. First, I’m going to need this young man.”
“No!” Sam said again, struggling against Gorman’s grip.
“If you want to see him again, you will meet me at this location at midnight,” Gorman said, handing MacGyver a card with a name on it. “Bring no one. Bring nothing but yourself.” He grinned down at Sam, pushing the gun harder against his temple. “He’ll be alive until then. If you don’t show up…well, I don’t need to mention it, do I?”
MacGyver felt helpless as he looked at the pleading look in Sam’s eyes. He couldn’t overpower the men. There were too many, and they were huge. Besides, even if Sam wasn’t his son, he still wasn’t about to gamble his life. The young man had been contrite and really seemed to want to help. All he could do now was play this twisted man’s game and try to get him back safely so he could testify.
“What is this all about?” He asked.
“I’m sorry, MacGyver. The time for questions is over. Just meet me at that location at midnight,” Gorman said.
All MacGyver could do was watch as Gorman dragged Sam away, his men following him.
To be continued…
"If a man does not keep pace with his companions, perhaps it is because he hears a different drummer."
--Henry David Thoreau
brains+brawn+beauty+personality=MacGyver