If I'm posting this, it means that the season did NOT end the way I thought it should have, Thornton-wise anyway, so I wrote this contingency story of how I thought things should have turned out. Or heck. Maybe things did turn out OK and I just wanted to post this anyways... guess that means you gotta go watch the episode! ;) XD

Yes, I know, Nikki is a part of this story *hiss* I kinda didn't like myself cuz I had to add her in. You couldn't really go anywhere with Thornton and not have Nikki, but we've seen Nikki all of three times I think? So if she's OOC, it's because of that ;)

Also, this first chapter is pretty long, but I'm not gonna promise that the other chapters are gonna be as long. In fact, I can almost promise that they won't be XD

Okay, I know that Jack hasn't actually told us what happened between him and Matty, but for this story, we're going to pretend like he did...

Jack walked into the war room, searching for his friend. He spotted the blond, but was slightly concerned when he saw the look on the kid's face. "Hey," Jack said, sitting down next to the troubled-looking MacGyver. "What's eatin' ya?"

"Nothing, I'm fine," Mac brushed off his friend's concern, not sure if he wanted to voice his thoughts out loud yet.

"Remember how you wouldn't stop bugging me about what happened between Matty and me?" Jack asked, poking his friend in the arm. "That's gonna be me this time," he informed the blond. "I'm just gonna keep bugging you till you tell me what's goin' on in that big brain of yours. And you've heard me, I can go on for hours and hours and hours. I could serenade you, I could quote all of the Die Hard movies, or any Bruce Willis movie for that matter, and it ain't gonna stop until you tell me what you're thinkin' about," Jack insisted. Mac raised his eyebrow at his older partner, almost in a challenging manner. Jack got an evil glint in his eyes.

"To all the girls I've loved before," Jack began with a smirk. "Who travelled in and out my door; I'm glad they came along! I dedicate this song to all the girls I've loved before-"

"Really?" MacGyver said with a laugh. "All the popular Willie Nelson songs you could have chosen from, and you choose that one?"

"Hey, he and Julio Iglesias made the song work, man," Jack insisted. "Such different voices, but when you put them together, it just...worked. Can I keep going?" Jack asked.

"No, no," Mac said, pretending to beg. At least, mostly pretending. "Alright. I'll tell you what's bugging me," he caved. "Because that's what family does; we tell each other what's wrong, and we don't take months after we meet our new boss to do so," he added, elbowing his friends in the ribs.

"Aiyee," Jack said, shying away from his friend's knobby elbow. "I finally told you, didn't I?" he asked incredulously.

"Took you long enough to do it though," Mac reminded him.

"Eh, debatable. Anyway, tell me what's wrong," Jack said, turning to face his friend more fully on the couch.

"I've got a date with Nikki tonight," Mac admitted.

"Wait...so I chose the right song to serenade you with!" Jack exclaimed with a laugh. "But that's not a face that says you're happy about your plans with her," he pointed out, referring to the expression that had taken residence on MacGyver's face.

"It's just… I dunno Jack. Something's just felt...wrong ever since she came back, I guess," he finally said.

"Well, it's probably because you're having conflicted feelings," Jack said. "You were so relieved to get Nikki back, but the cost of her coming back was finding out Thornton, the boss who seemed like she always watched our backs and was always there for us, was a mole. That'd make me have mixed feelings about my old girlfriend for a little while too, but seriously Mac. It's been months, and you've seen Nikki all of two times since she got back, at least to my knowledge," Jack said. "You've gotta face the feelings sometime, brother."

"It's not that," Mac said. "Or at least, not completely. Call it a gut feeling Jack, but something just isn't sitting right with me about this whole 'mole' situation. I think I've pushed it aside because I was just happy Nikki turned out not to be a traitor. I was willing to overlook things, but the more I look at it, the less comfortable I feel with everything. I also got a call from the prison," Mac added. "They told me that Thornton wants to talk with me as soon as I can."

"Why?" Jack asked, scrunching his face up in confusion.

"How am I supposed to know?" Mac asked, rolling his eyes at his partner. "My guess is that's what I'm supposed to find out when I go talk to her," he added sarcastically.

"Wait, you're not actually gonna do it, are you?"

"I think I will," Mac replied. "I mean, what can she do to me? We'll be in a secure facility, with guards around us. I don't think I'll be in danger," he pointed out.

"When are you gonna go?"

"I was thinking Monday."

"Any particular reason for the wait?"

"Well, there's the thing with Nikki tonight, and then I want to have the weekend to make sure my head is clear and I'm thinking things through logically," Mac replied.

"Fair enough," Jack said. He could still tell his friend looked troubled though, so he continued talking. "Listen," Jack said, putting a hand on Mac's shoulder. "Go see your girl tonight. I'm sure your conflicted feelings are all just a form of survivor's guilt," he tried.

"You...you do know what survivor's guilt is, right?" Mac asked, staring at his friend while raising one eyebrow.

"Yes I know what survivor's guilt is," Jack replied drily. "Like I said-a form of survivor's guilt."

"Whatever, man," Mac relented with a chuckle.

"But you're gonna go see Nikki tonight?" Jack asked, staring at his partner intently. Mac nodded his head.

"Yeah, I'll go," he said.

"Good," Jack said proudly. "But remember," he cautioned, wagging a finger playfully at his young partner. "Don't stay out past midnight, otherwise you get turned into a pumpkin!"

"I'll do my best," Mac replied, putting as much sarcasm into his response as he could.

"I'll see you tomorrow," Jack said. "Try and forget about everything except you and your lovely lady tonight," he said, pointing a finger at his friend as he stood up to walk away. Mac watched his partner walk out of the war room, and he heaved a sigh. He could only hope that Jack was right, and that all this worry was just his overactive brain trying to find the loophole in every situation.

0-0-0

"Mac?" Nikki said, putting her hand over Mac's on the table. He looked up, slightly startled.

"Sorry," he said, letting out a deep sigh. "Just got a lot on my mind," he admitted, giving the blonde woman a small smile.

"Hard mission?" she asked with a gentle expression.

"No, just thinking about something," he tried assuring his once-upon-a-time girlfriend.

"You can talk to me, Mac," Nikki said, rubbing his hand a little. Mac shook his head.

"Honestly, it's nothing," he insisted. "Let's just get back to dinner," he suggested, picking up his knife and fork to cut into the dinner their server had brought a few minutes before.

"Mac," Nikki said again, slanting her mouth and giving him a disappointed and pouty look. "You've been avoiding me ever since I got back, and I get it. I hurt you more than you ever deserved to be, both emotionally and physically," she said. "After everything that's happened in your life, I did exactly what you have always been scared of someone doing: I left you," she admitted. Her eyes filled with tears and she grasped his hand again. "I am never going to be able to apologize enough to you for what I did, but let me try to start mending our relationship," she begged. "Tell me what's wrong."

Mac observed the woman across the table from him, and a memory of a similar scene danced in front of his mind. The memory was of a diner, him and Nikki, and the table decorations he had created with the utensils they weren't going to use. The only difference between then and now was that last time, there had been agents from Nikki's organization surrounding them inconspicuously, and oh yeah. Nikki had been pointing a gun at him from under the table. He resisted the urge to check for a hidden gun, reminding himself that both of Nikki's hands were on the table, holding his. He mentally shook his head, convincing himself that Nikki was right, and that he was overreacting.

He opened his mouth to tell Nikki he had been thinking about Thornton, but another memory from the same night at the diner stopped him. This memory was of the conversation had taken place.

"Murdoc failed, but the next person they send won't. No one will be safe; you, Jack, my replacement...Bozer."

Mac straightened as he realized something.

"Do you remember what happened to Berkhoff?"

"Yeah, he was killed in exfil; his helicopter was shot down."

"Who told you that? Thornton?"

"Mac?" Nikki asked, bringing the young man back to the present. He looked at her, drawing back a little bit instinctively. "Mac, what is wrong with you today?" she asked, sounding both concerned and slightly snappy...as well as a little suspicious. Mac shook his head; he couldn't think straight-nothing was making any sense. He had to get out of there.

"I'm just not feeling very well," he informed her. It wasn't technically a lie; he was feeling confused and slightly sick to his stomach, though he knew it wasn't because of some bug. "I think I need to go home," he said in an apologetic tone. "I really am sorry," he said as he stood up. Nikki's face was a hard mask of emotions to read as she stood up with him.

"Well, I could take you home if you're feeling sick," she offered, grabbing her purse and her keys.

"No, no," he said, shaking his head and giving her a smile that he hoped didn't seem too forced. "I'll be fine to drive home; I don't want to get you sick."

"Mac, I said it earlier: I know I screwed up. I'm so sorry if it's making it hard for you to see me," she apologized again. "I want to make it up to you," she insisted. "Tell me how to do that!"

"I just...I think I just need a little more time," he finally said as they walked out the door of the diner.

"Okay," Nikki said meekly, grabbing his hand and rubbing it. "Just let me know when you think you can see me," she implored.

"I will," he promised. Nikki looked like she wanted to go in for a hug or a kiss, but Mac simply turned and walked towards his jeep. He climbed in the driver's seat and started his car, glancing at the young woman in his rearview mirror. She was staring at him with a disappointed look on her face, but he knew he had to think things through on his own, without her being there to distract and possibly persuade him one way or another. He put his jeep into drive and pulled forward, glancing back at his ex just in time to see her pull out her phone and hurriedly begin to type something. He took a deep breath.

I have to relax. It could be anything. I have no proof that she's doing anything besides what she says she's trying to do, which is fix whatever relationship the two of us have now. What I do have is hard, solid proof that Thornton is Chrysalis. That should be all I need, right? So why do I feel like something is wrong?

0-0-0

Mac sat by the fire pit, staring at the dancing flames, lost in thought.

"Mac? Mac!" he heard someone calling out to him. He jerked slightly, looking up and realizing Bozer and Jack were standing there, staring at him with intense looks. "You back with us, brother?" Jack asked.

"Yeah, I'm good," MacGyver said, bringing himself the rest of the way out of his zoned-out state. Jack gave him a skeptical look, but Mac changed the subject before Jack could ask him about his date with Nikki. "You guys ready to watch the game?" he asked with somewhat-faked sounding enthusiasm. There was a football game going on, and the two teams playing were the two that Jack and Bozer both rooted for, so there was a mostly-friendly rivalry going on between them; Mac was simply there to enjoy the game.

"Oh yeah," Bozer cackled, rubbing his hands together. "Your team's going down, Jack!" he said, jabbing the older agent in the chest with a finger before he turned and walked back into the house. Jack rubbed the spot where Bozer had poked him, chuckling and shaking his head slightly. He looked back at Mac, and the blond knew the next question that was going to be coming out of his friend's mouth.

"It was fine," he lied before Jack could even voice the question. Jack quirked his eyebrows at his partner skeptically.

"See, I think I'd be more inclined to believe you if you didn't look like your favorite chemistry set had just been stolen," Jack pointed out as he sat down next to his friend. "What happened?"

"Nothing," Mac tried convincing his older partner. "We went, we ate a little, and then we left. That was it," he insisted. Jack stared at his partner, not believing him for a second.

"Come on, man," he prodded again. "How much have we been through together? And you expect me to believe that you're alright, when clearly I can see that you aren't?"

Mac sighed; he knew Jack wasn't going to let it go, so he finally decided to confide in his partner. "Just...while I was with Nikki, it reminded me of when she confronted me in the diner, after we caught Murdoc. Our conversation from that night started going through my head, and I realized something. She left Thornton out."

"What do you mean, 'left her out'?" Jack asked, brow furrowing in confusion.

"She told me that even though Murdoc failed, the next person her team sent wouldn't. She then said that none of us would be safe, mentioning each of us by name, except for Thornton."

"Okay? So maybe she just forgot to mention her," Jack argued. "That doesn't mean that Thornton's innocent," he pointed out.

"Like I said, it's just a hunch I have; I don't have any proof," Mac conceded. "But there is one more thing that isn't sitting right with me," he added, looking over at Jack.

His partner looked at him with an expectant expression. "Well c'mon, man, don't leave me hangin'!"

"That night at the diner, Nikki also brought up Berkhoff and asked me if I remembered what happened to him."

"Wait, wasn't he in the chopper that got shot down during exfil?" Jack asked in clarification.

"That's what I said," Mac agreed. "But when I said that, Nikki asked me if Thornton had told me that."

"Well, she did," Jack confirmed. "Wait, are you saying what happened to Berkhoff wasn't an accident?" Jack asked suddenly, enraged. He hadn't known the agent very well, but if Thornton had arranged for him to die, he was not going to be happy.

"I don't know," MacGyver said, trying to calm his friend down. "Nikki didn't say specifically whether Thornton orchestrated it or not. But listen," he insisted.

"Sorry," Jack said, motioning for his friend to continue.

"Nikki made it seem like Thornton was someone to be wary of months before she came out from under her CIA cover, right?"

"Right…" Jack said, realizing he could see where the kid was going with this.

"So why did she seem so shocked when we discovered Thornton was Chrysalis?"

"Maybe she had her suspicions, but she didn't want to believe them herself," Jack tried reasoning.

"So why wouldn't she just tell us her suspicions when she came out as an undercover agent?"

"Would we have believed her?" Jack asked, raising his eyebrow at his friend. Mac considered his friend's argument before he sighed, shaking his head.

"No," he admitted. "But something just isn't sitting right with me," Mac repeated, rubbing his forehead with his hand. "I can't explain what it is, but something feels wrong."

"I don't know what to tell you man, except to trust your instincts. If you think there might be something there, do a bit of digging," Jack encouraged his friend, knowing this was just going to continue to eat the kid until he did something about it.

"Thanks Jack," Mac said.

"That's what I'm here for," Jack said. "To bestow my vast knowledge on you younger generation," he added with a wink. Mac rolled his eyes, but Bozer yelled at them from inside the house before he could respond.

"Guys, are you coming?" the two of them heard Bozer yell from inside. Jack and Mac looked at each other and shared a smile. Jack stood up and held out his hand, helping his young partner to his feet, and the two of them walked inside to watch the game.

"Get ready to lose your money, Bozer," Jack said with a wicked smile. "There's no way my boys are letting me down; they're on a streak, and they aren't about to lose to some all-star wannabes," he goaded. Their (mostly) playful fighting was called off within a minute of the game starting though as all of their phones began buzzing incessantly. Mac looked at the screen, realizing it was a text from Matty to all of them. He looked at his two friends, who had concerned and slightly grim looks on their faces.

"Guess we'll have to catch this on DVR," Jack said disappointedly, reaching over and hitting the record button on the remote. "Let's get over to HQ," he said as he set the remote back down.

0-0-0

"Riley, you got the message too?" Bozer asked as they met up with the young woman right outside the Foundation.

"Yeah," she replied. "What do you think was so urgent that Matty had to call us in on a Saturday? Especially since we don't have another op for a few days," she added.

"I don't know," Mac replied as they walked in the building. "But whatever it is, Matty's text sounded urgent."

"Yeah, and it's hard for a text to sound that urgent," Jack added.

"Not for Matty," Riley pointed out.

"Yeah well, not a lot is hard for that woman," Jack argued.

"I thought you two were getting along now?" Bozer asked.

"Oh we are. Doesn't mean she doesn't scare the living-" Jack was cut off as the elevator doors opened, revealing their boss standing there, a look of both worry and frustration written all over her face.

"Good, you're here," she said, sounding more snappy than she usually did. "Took you all long enough," she added.

"Sorry Matty," Mac apologized before Jack could make a snarky remark that would probably only succeed in making their boss more agitated than she already was. "What's going on?"

"Need us to take out a terrorist cell? Is there a threat to the life of the President? Do we get to protect some lovely government women?" Jack asked, barely pausing for breath between his questions. Matty turned and stared at Jack with an unamused expression.

"No terrorist cells that I know of, the Secret Service takes care of the President, and I wouldn't put any woman through the torture of having you as their body guard," she shot at the older man. Jack put his hand over his heart in mock-hurt. "This is something more personal," Matty continued, looking at all of them with what MacGyver would almost call pity in her eyes.

"Oh no, Matty," Jack said, all joking gone from his voice. "I'm so sorry," he said sincerely, remembering what had happened the last time Matty had said that a case was more personal. Matty looked up at him, confusion and then frustration coming over her face.

"It's not personal for me," she clarified. She stared at the four confused and slightly worried agents around her. "I just got a call from the CIA facilities that Thornton was being held at."

Mac's gut sank, and he knew what the next words out of her mouth were going to be even before she said them.

"Patricia Thornton has escaped custody."

Ah, but did she really escape, or did something more sinister happen? 0.0