The Autobot shuttle flew farther away from Canterlot, going farther and farther to the west side of the United States, all the way back to the Autobots base in Nevada.

Inside the shuttle, the atmosphere was nothing but somber and sad. Sunset Shimmer was hurt, they had lost more warriors in one day than they did in an entire battle, and now Optimus Prime was gone. Things weren't looking particularly great for the Rainbooms, or the Autobots.

All on the ride back, Twilight held Sunset close to her, and she didn't let go. Twilight's body felt cold, and her lips were trembling. Sunset's heart was still beating, but she was scared out of her mind.

Applejack who sat on the seat next to Twilight frowned. And unlike Twilight, she was trying to keep herself calm and composed and not burst out crying at the sight of one of her friends who could possibly dead.

She patted Twilight's shoulder, "Sunset will be alright Twilight. I'm positive."

Twilight whimpered and sniffled, "I hope so..."

Tears welled up in her eyes, and she saw a sliver of white near her left eye. Applejack had offered her a tissue. Twilight accepted and she wiped away the tears from her face.

"T-Thank you..."

As the shuttle rocked, one of the students looked towards one of the Bots that sat down across from them.

"Where are we going?"

"We're going back to our base of operations," Tracks replied.

"But Sunset needs medical attention," Flash interjected. "She needs to see a doctor."

"Mr Sentry, I can assure you we have a medical center specifically for humans. And we have a Mini-Con who's been trained for these kind of medical emergencies as well," Cadet Strongarm replied.

"Good. As soon as we get off this... shuttle, we're taking Sunset directly to the medical center." Rarity sternly said. "No questions asked."

The two recruits gave affirming nods.

Half an hour went by, and everyone was still wondering when they were going to arrive back to the base of origin. Everyone, particularly the humans, were acting very antsy while they were sitting in chairs strapped in for the ride back. They were in desperate need to stand up and stretch their legs.

"Ugh, how much more do we have to wait? Trixie needs to stretch her legs!"

Just then, a voice spoke over the loudspeaker.

"Good evening everyone, this is your pilot Shadow Flame speaking. I'm going to go ahead and put on the 'fasten seatbelts' sign as we make our way into the Mojave Desert, Nevada. Thank you for flying Autobot Airlines."

The shuttle slowly went down towards the ground, aiming its nosecone to the runway that was clearly marked and visible for the shuttle to see. Its landing gear folded out, gears turning and changing.

The shuttle moved closer to the runway, and its rubber wheels made a tiny bounce as it landed, driving down the runway and going right inside of the base hangar. The interior of the shuttle shook and bounced the crew that were sitting onboard, rattling the gear and the crew within its hull.

"Evvvverrrryttthiiinnnggg isssss sssshhhhakkkkiiingggg...", Flash's teeth chattered.

The shuttle's interior continued to rattle and shake, sending the humans flailing all over in their seats, and even throwing a few of the Autobots around, making any ability to hang onto the seats or the handlebars impossible. Some of the crew even fell onto their backs, their chests, or even onto their sides only to be crushed under the weight of more crew members.

"Ah! Who taught you how to fly!?" Applejack yelled as another Autobot fell right smack down in front of her.

"Hey, I've only been a spaceship for three months, and I've barely got the practice for landing!"

As soon as the shuttle drove on more runway, it began to slow down as it drove right into the hangar of the outpost. The minute they were inside, the hangar doors immediately closed behind them with a very loud SLAM.

Ratchet and Wheeljack were the only ones to approach the shuttle, both running right towards it.

"Shadow Flame, glad to see you made it."

Shadow Flame said nothing. He didn't think of anything to say to the doctor that would be good. He knew that the two wouldn't be too happy to hear what had happened out in the battlefield.

"Um... Shadow? Aren't you going to tell us how the battle went?" Wheeljack asked.

"I'm just gonna let our crew members tell you."

The door opened up, along with a ramp for them to walk down on.

"Okay, so lets see who came back...", Wheeljack said with a control pad in his hand.

As soon as the group began descending from the shuttle, Wheeljack began marking off each and every person that came out.

"Quickshadow. Arcee. Strongarm. Tracks. Wasp. Road Rage. Highbrow. Outback. Blaster. Smallfoot. Hound."

Wheeljack looked down and he noticed the humans walking out as well. Ratchet glanced back to Wheeljack, who just shrugged.

"So we have some students from Crystal Prep and Canterlot High here. No problem, I can count them too. Lets see... Jet Set. Upper Crust. Neon Lights. Trenderhoof. Royal Pin. Suri Polomare. Fleur De Lis. Trixie Lulamoon. Micro Chips. Sandalwood. Flash Sentry. Lyra Heartstrings. Bon Bon Drops..."

Wheeljack kept checking off each person who came off the shuttle, and soon it came down to the last few people.

"... Indigo Zap. Lemon Zest. Sugarcoat. Sunny Flare. Sour Sweet... oh, hey girls! Glad to see you're back safe and sound."

"Yeah... safe...", Pinkie said somberly.

Wheeljack raised a brow, "Pinkie? Why are you sad? You're never down when you come here."

"This time... things just got worse...", Pinkie sniffled.

Twilight was next to follow after, still holding Sunset Shimmer in her arms.

Wheeljack and Ratchet's eyes widened.

"Oh Sweet Solus! What happened to her?" Ratchet nearly shrieked.

"She's hurt! Is Fixit in the medical bay? She needs attention!"

"Yes, please, go right ahead," Ratchet said, letting them go by.

Twilight ran off with Sunset held in her arms. Once she was gone, the final crew members walked off the shuttle.

"Okay, final ones... Ironhide. Knockout. Bumblebee. Jazz. Sideswipe. Perceptor. Ultra Magnus...", Wheeljack looked back up to see who else was stepping off, but there was no one left.

"Wait... where's Optimus?"

The shuttle transformed to the mech it was disguised and it shrunk down back to its normal size with the rest of the Autobots.

"Shadow, where is Optimus?"

Shadow just looked at them with a sad look and shook his head before walking away on his own.

"W...What happened?" Ratchet asked. "Somebody say something!"

As everyone slowly walked together further into the base, they noticed some familar faces start to walk towards them. The rest of the Autobots were still here in the base. Some faces they recognized were the Dinobots, along with Blurr, Hoist, Grapple, and many others.

"Howdidthemissiongoguys, huhhuhhuhhowdiditgo?", Blurr asked real fast.

"Blurr, calm down," Indigo said without any interest.

"Girls? Are you alright?" Pipes asked.

"I don't feel like talking right now...", Lemon sadly said.

The Crystal Prep girls walked slowly away with their guardians right behind them, and the rest of the teenagers followed suit. But they all stopped when the girls in front of them turned around to face them.

"You guys are free to hang out in our lounge... apartment... area. Just third corridor down the left. Its a place specifically designed for us mortals."

"Fine by us," Trixie said.

"There's also lots of beds in there if some of you need rest. Beds, bathrooms, kitchens, work rooms, gym equipment, its got everything for you guys to chillax," Indigo replied.

"Sweet. Come on guys, lets go chill," Vinyl said leading the group away.

"I'm gonna start cooking dinner. I've got a big order to fill for everyone," Sandalwood said as he walked away.

"I'll offer a hand to you my good sir," a Crystal Prep student said.

As soon as they walked away down more hallways, it just left the girls and their guardians to sit still for now. All of them let out a heavy sigh.

"So... what do we do now? Without Optimus, we're dead," Indigo asked.

"Hang on Indigo. I know Optimus isn't here, but we've survived much worse situations without him. Heck, in the first few weeks we met Sunset and the girls, Sunset actually took over for the team while and it turned out fine."

"I thought the only reason you were victorious was because Twilight came for you all at the last minute and saved your butts," Sugarcoat bluntly said.

Hound glared at Sugarcoat.

"The point is... we've been through worse, and we always make it out of a bad situation. We can do it. We just need to do something to get our minds off. Come on, maybe we can do some training or something," Hound asked.

"Actually... I wanted to talk to the girls in private for a moment first, if that's alright with all of you."

"Um... sure, I guess," Hound replied, "Fellas?"

The bots all gave nods.

"Come on, lets leave the girls in private for a bit," Hound said, leading the group away.

Once it was clear, Sour Sweet pulled the girls all close together.

"Thanks girls. I just wanted to talk alone to you guys."

"Are you alright Sour?" Sunny asked.

"I am, but... I wanted to ask your advice on something. I know we just went through an entire battle today, but... I wanted to ask you all something that's sort of, not related to that."

"Given our current situation I think our primary focus should be on our situation that we're now back in war, but go on," Sugarcoat replied.

Sour nodded, "I will, but I just want some advice from you guys right now. I, um... got a little something in my pocket that I saved but... given our current situation, I'm not sure when I'm going to bring it up."

"Bring what up?"

"Well...", Sour hesitated.

She reached into her left pants pocket and she pulled out a small little box that fit into the palm of her hand. And when she pulled the top up, it revealed a small shiny green emerald on a ring, eliciting a gasp of shock and surprise from the girls.

"Oh this is serious dude...", Lemon murmured.

"Sour, are you actually, positively, indefinitely sure you want to--"

"Yes, I do. Look, I know tensions are high right now, and I'm not going to bring this up to Smallfoot right now but... I do want to take things to the next level. I know I'm only close to finishing high school, and we haven't gotten far yet with finding a job or a future, but if something ever happens to us... I want to at least know I was able to put this ring on her hand. So that, if something ever happens to me, she'll at least have a part of me with her... forever, and ever..."

Sunny smiled to Sour.

"That's really sweet of you Sour. But, what about--"

"Actually, that's why I got two," Sour said, pulling out a much bigger ring from her coat pocket. Big enough to fit onto Smallfoot's red finger.

Lemon's finger went up and so did a confused face.

"How did you fit that in your coat?"

"Don't ask. The point is... should I?"

Sunny and Indigo shared a look to one another, and then glanced back to Sour.

"I say you do it, when the time's right. Which is most likely not now, not here, and not in the middle of all of this drama. But if we can, how about we just focus on trying to mend what has been broken, and try to recover from what we had just lost today?" Sugarcoat replied.

"Agreed," the other girls quipped.

Lemon Zest walked away with Sugarcoat and Indigo Zap, leaving behind Sunny to talk to Sour Sweet. Sunny looked to Sour with a warm smile.

"I'm not saying its a bad idea dearie, but maybe you want to think about this some more before you make any decision. I'm not going to deny that I think you two are absolutely perfect together, but are you sure you absolutely want to do this?"

Sour just took a moment of silence to give some thought, and responded with a resounding 'yes'.

Sunny nodded, "Alright. But, I do want you to take some time to think about this. Don't rush it, don't spring this out of nowhere. Do it when you think the time's right."

Sour smiled, "I will, and I promise. Thank you."

"Now come on, lets go see what Hound has planned for us in the training center."

Sunny and Sour both grinned and the duo walked together, catching up with their gaggle of friends with smiles all around. At least the comfort of their friends was here to help them.

Over in the medical center of the base, Sunset Shimmer was now placed into a bed now only wearing a hospital gown. There was an IV unit going directly into her arm, some bandages over her wrist and one that was hidden was one wrapping around her stomach, a band-aid over a part of her forehead, and several visible bruises. And off to the side was a scared Twilight and her friends, who just watched as Sunset lay lifeless and cold, all the while the single beep of a heart-rate monitor was the only sound they heard.

"S-She's going to be okay... right?"

To the right side of the bed, was a little orange robot who was roughly the same height as the girls who held a little clipboard in his hand.

"Sunset will be okay, although she will need some help recovering from her injuries. And as for the Matrix... I'm not sure what we should do with that," the Mini-con Fixit said.

Lying on the bed with Sunset was the Matrix of Leadership which they had shrunken down to their size, allowing it to be tucked under Sunset's arm.

"As far as I know, Optimus specifically said the Matrix was to be guarded by her. If he trusts her with it, I say we just let it stay with her," Applejack replied.

"At least she's got it safe with her like her teddy bear," Pinkie replied, sniffling.

"Lets just let her get some rest. I'm sure she'll be alright by then... I hope," Applejack frowned.

The girls all gave a few nods and one by one, they began to walk away, leaving Sunset by herself to get some much needed rest. All except for one...

"Twilight? You comin'?" Applejack asked.

"If its all the same with you girls, I think I'm gonna stay here to keep an eye on her," Twilight said, sitting in the chair next to her bed.

"Alright, well, we'll come back to check up on you," Rarity replied, "Come girls, perhaps we should break the news to everyone who's in the dark."

The girls left Twilight to keep her company to Sunset while the five of them walked to one of the main rooms to meet with Ultra Magnus, to help explain their unholy predicament.

"May I ask why you haven't told us anything yet?" Ratchet asked.

"It is my belief that Sunset's friends here will provide some better input than me," Ultra Magnus said before looking at them, "Go ahead."

Rainbow sighed.

"Optimus is having Sunset Shimmer watch over the Matrix of Leadership because he's... he's... gone."

Ratchet and Wheeljack's eyes widened.

"He's--"

"We don't believe he's dead, but... he gave his final order. And that was for all of us to protect Sunset and the Matrix of Leadership at all costs."

Ratchet was flabbergasted.

"You mean to tell me, that the only one who kept our team functioning after so many years of losses and failures is now gone... Ultra Magnus... we needed him..."

"It doesn't matter at this point Ratchet, what's done is done," Rainbow huffed.

"But what do we do now!? With Optimus gone, with half of our soldiers and friends gone, all we have is just... us!"

"Ratchet, calm down! I'm worried too, but there's one thing you're forgetting here. We have Sunset," Wheeljack intervened.

"And what good does that do!?"

"Sunset Shimmer took over as temporary commander when Optimus was out of commission, and she's been doing a fine job taking over whenever he wasn't around. As far as I'm concerned, Sunset is team leader."

"Excuse me, but I don't mean to offend, but what good is a small human in charge? They can be crushed easily in one step. Their skin isn't impenetrable like our metal plating," Ultra Magnus replied, crossing his arms.

"Which is why they wear the protective armor to keep themselves from danger," Wheeljack interrupted.

Ultra Magnus looked down to Principal Celestia, "With all due respect ma'am, I respect Sunset Shimmer as a soldier and a close friend to Optimus... but to put all our trust, our problems, and our leadership to a small child isn't such a good idea."

"And what do you know about leading?" Pinkie screeched.

"I was Optimus Prime's second-in-command during the war, meaning if he wasn't around, then that means I was in charge. But I'm still not sure if we should put all of our--"

"Listen up here bub!" Rainbow snarled, "If Optimus put her in charge, then she's in charge. The only people we listen to is Sunset, Ratchet, and Optimus Prime. No one else is charge of us, and that means you!"

Ultra Magnus was unfazed, and he just glared at Rainbow Dash.

"Uh, she is right about Sunset being in charge...", Fluttershy whimpered.

Ultra Magnus scrunched his face and tapped his finger on the side of his head.

"Very well. If Optimus put her in charge, then I suppose she's in charge. But until she wakes up, I'm in command. And as first order, we need to seal off all of the doors and set for lock-down. We cannot allow the Decepticons to detect us nor find us. Sunset Shimmer needs our 100% protection, and that means until we come up with a plan to transfer her to a safer location, no one and nothing is to leave this base. Now is everyone else who's remaining all here and accounted for?"

"I did a personal check of all of our remaining crew members, we are all here and accounted for," Knockout grinned with a smug look.

Rarity smiled to Knockout.

"Very well done," Rarity beamed.

"Yes. I am just that good."

"Save your boasting for later, Knockout. And I would also appreciate it if you could tone down any boasts or complaints of any damage to anyone's or your own finish."

Knockout just sneered, "Very well then, Herr Kommandant."

Knockout walked away muttering something incomprehensible that Ultra Magnus couldn't hear, but the former second-in-command didn't care.

"So... what do we do now?", Fluttershy asked.

"I would suggest we check in on the rest of the Crystal Prep and Canterlot High students that came with us. I'm sure we may need to set up some living arrangements for the time being since we won't be leaving anytime soon," Rarity said.

"Agreed. We need to make sure comfort is provided for all of them while we're here," Ratchet replied.

The girls were given their excuse to leave and to go and talk to the rest of their possible bunk-mates while the other four that were standing remained in their own conversation.

"Wheeljack, Ratchet, set our base into lockdown mode. We need to ensure that we do not become detection. If we are to carry Optimus's final orders, we need to ensure every ounce of protection and security measure we can to keep Sunset Shimmer safe."

The two soldiers nodded and they moved to the control console and began accessing the mainframe, beginning to turn on the security and defense systems. One by one, each of their defense mechanisms began to turn on, and security began to kick up.

Leader-1 looked to Ultra Magnus who didn't seem to look like he was looking at anything.

"I'm going to check in with the rest of our soldiers. Maybe there's something we can do in the meantime to find a way to keep Sunset safe," Leader-1 said before walking away.

As the former Guardian commander walked away, Ultra Magnus was left alone in his thoughts. Protect Sunset Shimmer and the Matrix of Leadership at all costs. If that was Optimus's final order, then it was an order they were going to carry out and they weren't going to fail him.

Author's Notes:

After so long, this has finally been published! And now onto the part which makes me hate myself even though I shouldn't be hating myself to begin with. Joy.

---

What do you know, two more unnecessary side-stories has been thrown in. I'm so sorry guys, I've got so much crap crammed in here that is making this story a big mess.

Actually... is it? I have enough in here already, I don't want to make any more filler/padding that takes away from the overall plot. Some of what I have in here is just side plots, and I do hope they don't take away from the further story.

By the way, that whole thing with Sour Sweet? That's gonna come back again much later, and I know a particular place to play that in...