I'm so glad you guys like this story! It's been bouncing around in my head for a while.

Now, for why Sam's a girl. One, the Kirk factor. Will's a Starfleet captain, he's heard of Jim's ways around women. This will lead to fun times between Will and Jim later in the story on their way to Cybertron (much later on…) Sam's also a girl because the Allspark brought her back to life, along with Epps and Will. In humans, women represent life (who carries the babies?) so the one who's going to give life back to them is going to be a girl.

BrowneyedShammer, you can defiantly be the number one fan for this.

Also, any ideas for alien planet names? I need at least one for chapter twelve!

If you think I own either StarTrek or Transformers, there's something wrong with you.

First Contact II

Two Years Later

The Enterprise might be the best ship in the galaxy, but the Constellation wasn't too far behind. The crew members on the ship quickly became used to the conditions the captain set forth, and if they didn't then they left ship quickly.

Captain Lennox ran his ship like the marines of the early 21st century. Each crew member had a minimum level of self defense they had to know, and it was not mandatory. Orders were followed to the dot no matter what they were. Except sometimes Lennox would delete an order on accident or they would loose a feed in an ion storm and he would do what was right, not what was ordered.

While Lennox kept them from court martial's, Commander Epps kept the ship running smoothly. Epps made sure each and every shift was manned, and at the end of the month a new shift schedule was posted. He made sure they arrived on time to all locations, be that scientific explorations or meetings with the ambassadors while they negotiated treaties. But no matter what, Epps made sure the crew was looked after and treated well.

But the crew knew they weren't the strangest part of the commanding officers. The other officers were incompetent, which was why Lennox and Epps pushed them all so hard. No, the strangest part was the other commanding officer how wasn't incompetent.

Lieutenant Witwicky was the head engineer, and she was a miracle worker. She was the only sane one out of the three competent officers. When Lennox and Epps got it into their heads to create another insane rule for training, Witwicky would call them idiots and say in her calm voice 'Normal people don't know three types of martial arts Will. One is just fine.' Witwicky kept the engines running in tip top shape, but she was also in charge of the ambassador duties. To the crew's amazement, she'd created more alliance than Lennox ever had, and she'd done it with more class.

If the crew had to guess, Witwicky used to be an ambassador before becoming an engineer.

Usually the three officers could be seen in the mess, not the officers mess but the regular one, talking to each other like they were old friends. Honestly, if the rest of the officers weren't incompetent, then they defiantly would have beaten the Enterprise in best command crew.

Sam frowned as she scrolled down the report on her data pad. Will had just sent her the knew information about the upcoming alien life forms they would be encountering on their next treaties talk and was expecting Sam to come up with the treaty in a matter of hours.

"I'm going to kill him," Sam snarled as she stormed through the corridor of the ship. Crew members quickly jumped out of her way, many of them giving respectful nods to her as she passed. After two years, they had finally stopped saluting her.

"Honestly," Sam grumbled as she entered the turbo lift, "I know Will was in charge public relations for NEST before I took over, he should be able to do this. And with three hours before the meeting with the Enochians. I never should have taken this job."

Sam continued to grumble as the turbo lift doors opened and she stepped into the engine of the ship. She couldn't help the tiny smile that graced her face as she listened to the hum of machinery. Sam never told anyone, but she felt almost normal around machines, and if she imagined hard enough they sounded like the familiar click and whirl of the Autobots.

Sam placed down her data pad and looked around the engine room. It seemed to be running smoothly, but Sam always liked to check. Especially because the last time she didn't an explosion from the warp core burned off both of her eyebrows.

"Mr. McMillan," Sam called out into the raging noise of the engine room, "Please report the current condition of the engines."

McMillan ran over to her side, oil spread across half his face and a wide beaming smile, "Lieutenant Witwicky! Everything is running…smoothly. The warp core is in working order, the dilithium crystal is powering the warp drive, and there have been no explosions. …Recently that is Miss Witwicky."

Sam offered him a slight smile, "Thank you Mr. McMillan. Now, I'm very sorry to tell you this, but our wonderful captain just dumped a new treaty on me. I'm going to be unable to supervise this shift in engineering, so I was wondering if you could fill in for me during this shift?"

McMillan was practically vibrating with excitement, "Of course Lieutenant! Anything you'd ask, we'll grant!"

Sam shook her head before picking up the data pad and heading back towards the turbo lift.

"I'm buying everyone a round of drinks next time we hit space dock!" Sam yelled back over her shoulder, and the cheers coming from inside made her laugh as she went back to work. She walked through the hallway towards her room, eyes focused on the data pad.

Sam had nearly reached her room when the ship jerked. It's difficult to explain the feeling to anyone who had never been on a Starship when under attack. Imagine one minute your standing on a perfectly flat surface, and the next your against a wall, with the ground shifting away from you. That was the feeling of a Starship under attack.

And that was what Sam was feeling as she smashed against the wall of the ship. Sam's eyes narrowed, and where panic would have kicked in during her years as a human male back in the early 21st century. But now Sam really was the soldier Lennox had named her during the fight in Mission City.

So Sam dropped her data pad and sprinted back to engineering. As soon as the doors slid open, Sam immersed herself in the chaos of the engine room during a battle. Small fires would randomly break out through the pipes, explosions of sparks would shower them as the control panels were damaged.

Sam continued through it all, screaming orders as she struggled to keep her ship in one piece.

"Get the coolant on the warp coil!" Sam yelled, pulling off her high heeled boots and working barefoot through the hell of the engine room, "And whatever you do, keep the dilithium crystals intact! We need those for war capabilities! Do not lose…"

The rest of her sentence was lost as an explosion rocked through the ship. Sam didn't even have time to scream as a wall of fire came tearing at her. She simply dropped down and let the control system block the worst of the flames. But it didn't stop the control system from coming loose and smashing her into the wall of the ship.

Sam just groaned as her world faded to black…

The blackness fell away, and he was lying on the desert sands. His eyes landed on the Matrix of Leadership, and suddenly everything came rushing back. He had to save Optimus, that was the only reason why he was alive.

So he struggled to his feet and began to run again, this time without Megatron trying to kill him. So he ran, and climbed onto Optimus's chasis. Holding up the Matrix, he let out a scream as he plunged the Matrix into Optimus's extinguished spark.

The Prime's body rocked as he returned to life, and he was nearly thrown off. Only the giant metal hand kept him from falling to the ground.

'Boy,' he found himself staring into the bright blue optics, 'You returned for me.'

And Samuel Witwicky could only smile in relief…

Sam's eyes fluttered open. It had been a long time since she dreamt of her passed life, and they only came back up when she was in some sort of danger. Which was why Sam pulled out her phaser and set it to stun.

Managing to pull herself out from under the control panel, Sam surveyed the damage to her engine room. The fire from the explosion littered the floor, and the other engineers were lying on the ground, flames moving over their prone forms.

Sam gagged a bit as the stench of burning human (and alien flesh) hit her. It wasn't nearly as bad as when the NEST Washington D.C. was destroyed by Sentinel and the Battle of Chicago, but it was still horrible.

She dragged herself out from under the control panel, and stumbled across the engine room floor to the hallway. Pushing to door open, Sam stumbled until her shoulder hit a wall, and she dragged herself down the hallway ready to shoot the first thing she saw.

Sam struggled not to cry as she saw the dead and wounded lying on the ground. She wanted to stop and help them, but she couldn't. Sam knew she had to find Will and Epps and make sure they were alright.

But when she turned down the hallway, Sam froze. A figure stood there, bent over one of the bodies of a crew member. And the red shirt got Sam to recognize he was an engineer, one of her people.

Sam pointed her phaser at the intruder, because that's what it was. It wasn't in a Star fleet uniform and Sam never remembered seeing this figure, and she made it a point to know every member of the crew.

"Put your hand in the air!" Sam screamed, pushing herself off the wall and struggling to fall to the ground from the pain coursing through her body.

The figure, a humanoid Sam noted dully, turned to face her with something close to fury on its chiseled face. Sam struggled not to laugh. She had always been a fan of 21st century television shows, which was why seeing Hugh Lorrie glaring at her from across the hallway made it funny.

"And what do you intend to do with that?" the Hugh Lorrie impersonator snapped, raising at eyebrow at her.

Sam coldly flicked the phaser from stun to kill, "I'll vaporize you, you son of a bitch. Now get away from my engineer."

He gaped at her, "I'm saving this humans life!"

Sam let her eyes fall onto the form, and noticed the light greenish tinge to the skin and immediately recognized the ensign.

"You're killing him," Sam announced softly, keeping her phaser on the humanoid while approaching the body on the floor, "Ensign Hartford is half Orion. He doesn't have the same molecular structure as humans. If you try to fix him with a dermo regulator, it will cause his atoms to rearrange themselves and kill him because of where his heart is located."

It gave her a shocked look, before pulling its hands back as quickly as possible from the ensign. Sam took that as her cue, and slumped down next to ensign Hartford. Placing her hand on his throat, she felt for a pulse.

Sam let out a chocked sob, "He's been dead for hours. There's nothing to do for him."

Pulling away from the body, Sam returned her phaser to the humanoid's forehead, which was typically a direct kill, "State your name, and why you are here on the Constellation after a recent attack! Were you the one who caused this?"

It snorted, and Sam could feel the indignation radiating off of its person, "Do you truly expect one person to be able to cause all this damage?"

Sam narrowed her eyes, "Of course. I saw what Nero did to Vulcan. I know better than to underestimate individuals. So I'm going to ask you nicely one more time, who the hell are you?"

Standing to his full height, which Sam realized was a few inches taller than herself, he gazed at her with a piercing intensity, "My designation is Ratchet. I am an Autobot from the planet Cybertron. And I can assure you, I did not cause this damage. If you would be so kind as to introduce yourself?"

Sam had to keep tears from filling her eyes. It figured that after years of searching space for them, the Autobots find her at the most inopportune time.

Sam lowered her phaser, and slumped against the bulk head, "Lieutenant Samantha Witwicky of the USS Constellation, from Star Fleet. Planet of origin is Earth."

Sam could see the surprise and sadness in Ratchet's eyes when he heard her name. But instead of reassuring the old bot, Sam had to make sure that he truly wasn't a threat to the remaining crew.

"So Ratchet," Sam drawled as she drug herself down the hallway and towards the bridge, "Do you know what happened here?"

Ratchet fell into step beside her, and Sam struggled not to let any of the pain she was feeling show through to him, knowing that he was a medic and would keep her from completing her duties as a member of the crew.

Ratchet responded to her as they walked through the corridors, ignoring the flashing red warning lights, "A species known as the Ziacon did this to your ship. We made contact with them, and after learning that we refused to give them our technology, they decided to wage war against us."

Sam muttered under her breath, "You guys just can't get a break."

Ratchet made no sign of hearing her, but Sam knew he had, "Recently, the Ziacon decided to target our planet directly. But they could not harm the adult mechs, so they targeted a sparkling. The Lord High Protector's sparkling to be exact. They killed the sparkling, and we were forced to retaliate. The Ziacon fled to their home planet, and came across your ship while escaping the sparklings creators,"

Sam growled low underneath her breath, "So we got caught up in the crossfire? Is that what you're telling me?"

Ratchet looked uncomfortable when he nodded, and Sam didn't even try to hide the snarl that passed through her lips. She stormed onto the bridge, livid as Ratchet followed silently after her.

Sam only relaxed when she noticed Will sitting in the captains chair, looking as lost and tired as she felt. Sam ran over to his side and pulled her captain into a hug.

Will cradled her close, smoothing down her hair, "Damn it Sam, I'm taking you out of engineering. We heard the explosion and I thought you'd died."

Sam laughed weakly, "Sorry about that captain. I was heading towards the bridge when I ran into someone. I think they might be on our side."

"Good, I ran into someone who can help also. He's with Epps right now sending out an S.O.S," Will said, pulling away from her, then his eyes landed on her feet and an eyebrow rose, "Sam, where are your shoes?"

She shrugged, giving him a weak grin, "Lost them in engineering? Seriously Will, how am I expected wear high heels while working with the dilithium crystals."

Will just rolled his eyes before they landed on Ratchet, who was studying the communications board with interest, "This is the guy you met."

Sam nodded, "He says his name is Ratchet, and he's from Cybertron."

Will froze and Sam saw the effort he was using not to beam in excitement, "Then I guess we'll have to ask him a few questions while we wait for rescue to arrive."

Will stepped forward towards Ratchet while Sam slumped to the ground next to the captain's chair. She shut her eyes and dozed, not listening to the interrogation of the Autobot. She knew that Ratchet wouldn't reveal anything that was important, and they'd probably discuss the ships condition and any and all military aspects of the meeting.

Sam grunted as she felt a foot connect to her ribs.

"Well, it looks like Miss Witwicky died of boredom," Sam could punch Epps for sounding so smug.

"Indeed Commander Epps. Maybe you should kick her again to double check that she's still living?" And Will to for giving that wonderful suggestion.

With a groan Sam opened her eyes, and fixed a glare on the two members in command gold. She calmly flipped them the bird before stumbling to her feet.

"Aren't you just a ball of sunshine this morning Lieutenant Witwicky," Epps announced, before pointing at another humanoid figure in the room, "This here is Autobot Ironhide. He was sent here with Ratchet, who you already met, to check for survivors."

Sam hummed a bit as she clambered to her feet, making sure to tug her skirt down. She fixed the other figure, who looked a lot like Vin Diesel, with a stern look, "Are you sure these two didn't cause the attack captain?"

Ironhide snorted, "As if you would be alive if I had attacked your ship."

Will gave her a stern look, "Lieutenant, we are supposed to keep an open mind when dealing with new species. I understand the loss of your engineers is making it hard to focus, but I can assure you, these two did not cause the damage to ship."

And with that, Sam finally let herself relax. She knew that tears were welling up in her eyes, and that she looked strange in her ash smeared uniform, especially without any shoes on. Will offered her a gentle smile, while Epps ruffled her already ruined hair.

Sam took in a deep breath, before jumping straight into business, "Is anyone coming for us sir?"

Will immediately entered captain mode, causing Epps to stand at attention. Sam had to admit, her commanding officers looked impressive, especially when they had an audience.

Will took his seat in the captain's chair, and gave both of them a stern look, "I've made contact with the USS Enterprise. Captain Kirk has agreed to pick all survivors up and treat them on his ship. But there's now a catch."

Will turned to regard the two Autobots, who had been arguing to themselves while the humans talked. Will cleared his throat to get their attention, "Gentlemen, due to the recent attack on the ship, we will need to be speaking with the leaders of your planet to make sure that there will not be a declaration of war sent out from the Federation."

Ironhide snorted, "As if you humans could harm us."

Epps smiled darkly, "The Federation is not only composed of human members. In fact, Terran members of Star Fleet are the minority now."

Ratchet let a whirling hum, "We will speak with our leaders to set up an appointment to make sure no ill will happens between Cybertron and the Federation."

Sam stepped forward, "Both of you will need to remain with us the entire time, for security purposes you know."

Ironhide took a step forward, "You think you can stop me, punk?"

Sam had a feeling of déjà vu to their first meeting, but she couldn't act surprised now. Not when she had a duty as a soldier.

So Sam pointed her phaser, still on stun, at Ironhide's chest and snarled, "If that is a threat sir, I will fire with deadly force. Permission to fire captain?"

Will nodded, "Permission granted Lieutenant. Understand gentlemen, no harm will come to you as long as you do not threaten my crew. If you do that, I will personally kill you myself."

Sam could see the sadness in Ironhide's eyes as he regarded Will, "You are very dedicated to your men, aren't you Captain Lennox?"

Will nodded, "If I wasn't, I wouldn't be leading them right now."

There was a moment of silence, that was broken by Epps.

"Sam, where are your shoes?"

Sam sighed, knowing this would be coming up soon. It was going to be a long time before the Enterprise showed up to save her from these lunatics.

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