I am sorry if this isn't how the book is supposed to go, it is an Artemis Fowl and Holly Short fan fiction. No lemon, and will include some sad scenes. Enjoy!
Artemis found himself inside of some kind of machine. There was someone at the controls, moving the levers and pressing the buttons, but Artemis couldn't see anything. It was like he was the person. But then a screen appeared, at eye level, and suddenly, Artemis found himself looking at every LEP member, including Foaly, N°1 and other creatures. Their pictures were all crossed out with red lines, but five weren't.
Foaly
Holly
Trouble Kelp
Mulch
N°1
All of his friends.
Laughing manically, the person grabbed the controls and the screen changed once more, showing Holly Short, alone, sitting on her bed in the LEP headquarters, and then the person pressed a stretched out and sank into Holly's neck, and she tottered woozily, finally collapsing as the screen with the LEP members popping up, with one more red line.
A bright red line over Holly.

Artemis woke with a start gasping for breath as he flopped around the giant bed he slept in. He struggle for a minute, trying to find where he was. Artemis finally relaxed as he realised he was in his own home.

"Butler!" He called suddenly. Immediately, the massive man came inside of Artemis's room, panic etched on his face.
"When is the next time for us to catch a plane to LEP headquarters?" Artemis asked.
"Never a plane. Could you call Holly to pick us up?" Butler asked.
"Of course." Artemis responded. "If it's not too late."

"Holly?" Asked the voice belonging to Artemis Fowl.
"

Hey, Artemis. What's up?" Asked Holly Short, about to sit down on her bed.
"Don't sit down!" Artemis's panicked voice suddenly cried out.
"Um...?" Holly trailed off, inches away from the bed.
"Someone's tracking everyone underground." Artemis explained. "Is there any way Butler and I can get down there? I need to stop it, before... Before-"
"Before what, Artemis?" Holly cut in.
"Before he gets you!" Artemis screamed in exasperation.
"M-me?" Holly stuttered.
"And... And Trouble, Foaly, N°1, Mulch... You are the only ones left." Artemis recovered quickly.
Holly smiled quickly, allowing herself the quick grin. Standing up, she opened the fairy communicator, which connected to the other one she had given to Artemis.
"Better, we'll come to you. Are you still at the Manor?" Holly asked, grabbing her Neutrino and placing it onto her hip. It felt good to have it back.
"Yes. Where are you exiting? We can pick you up." Artemis said curtly.
"Tara, I think." Holly said, and then rushed out of the room, heading towards the LEP main office, which belonged to Trouble Kelp.
"Alright. See you." Artemis said, and closed off the connection.
What were you thinking? He chided to himself. You never show emotion. But, good response. He mentally congratulated himself.
"Butler, take us to Tara." Artemis commanded, glancing at Butler who was by his side.
"Of course." Butler replied, and proceeded to get the necessary items for their trip.

"Trubs!" Holly panted, facing towards the front desk.
"Captain Short, call me Trouble!" Trouble Kelp shouted.
"Artemis Fowl just contacted me. He said that we are in danger. We need to go see him!" Holly said, sighing quickly.
"Artemis Fowl this, Artemis Fowl that. What if it's a trap?" Trouble asked.
"We are being hunted. Someone has taken all of the LEP officers, including some of the additional, innocent People!" Holly cried. "Just give him a chance!"
"Fine. He gets 48 hours. Foaly?" Trouble asked the eavesdropping centaur.
"Yes, Trouble?" Foaly looked up innocently.
"It's not just us. N°1, Foaly, Mulch, and you!" Holly cut in.
"Looks like we're going back above ground!" Sang a dwarf who happened to be walking inside.
"Hello." N°1 said, walking in behind Mulch.
"I thought you were still learning?" Holly exclaimed, hugging the little warlock.
"Yes, but they let me get a month off. I heard we are taking a trip? Wherever to?" N°1 asked.
"Ever heard of Artemis Fowl?" Trouble asked.
"Who hasn't? He saved my people."
N°1 said.
"Yes... Well, Foaly, which shuttle can we take?" Trouble asked, walking over towards the centaur, who was extremely quiet.
"To Tara? Take the third one." Foaly responded, not like his usual, joking self.
"Foaly, what's wrong?" Holly asked asked Trouble left the room to get the shuttle ready.
"It's the kids. They are acting like they don't need me anymore." Foaly sighed.
"Don't worry! It's just a stage they go through." Holly said, and smiled a little. Cheered up, Foaly became his usual self.
"Shuttle three is one of the best models this year! I designed it myself, and it is perfectly safe." Foaly said, as the rest of them followed the centaur towards their shuttle.
"Well, let's see what it can do. Where's Trouble?" Holly asked, sitting in the pilot's seat.
"What's this?" Foaly asked, picking up a piece of paper.
"Let me see." Mulch reached over and snagged the paper, plucking it out of Foaly's hands.
"Thanks for the Commander. You can't evade me forever. Not now. Not ever! Gee, thanks for the optimism." Mulch muttered after he finished reading.
"Then we should better be going." Holly swallowed, suddenly noticing the sticky, red patches could possibly have been Trouble's blood.
"This shuttle hasn't been used since-" Foaly suddenly stopped, as he and Holly both knew who Foaly was talking about.
"Since Julius Root." Holly finished his sentence, swallowing the lump in her throat the best she could.
She clearly remembered the bright explosion, the ripping force created by Opal Koboi. Holly's hands tightened on the steering wheel, and Foaly casually reached over and lessened the pressure.
"Get us to some Mud Men." He said, smiling encouragingly, trying to lighten the mood.
"This is going to be a bumpy ride!" Holly said, and started the engine. The shuttle crashed along the tunnel, all of the passengers hurrying to strap themselves into the seats. Finally, they arrived at Tara, concealing the shuttle the best they could.
As everyone else went outside to breathe the air and chat with Butler and Artemis, Holly hung back and looked at the blood again.
Without thinking, Holly took a sample of it and scanned the blood. As the readings came back, she couldn't believe her eyes. Artemis came into the shuttle, took one look at her face, and rushed over to see the readings too.
"Julius Root." He breathed.
Root was already injured from who knows what, and yet he still decided to go on all those missions with Holly and Artemis- until the very end.
Until Koboi.
"Relax, Holly, we will sort it out." Artemis said, his breath hitting Holly's face as he tried to unclench her fingers from the blood tester.
"It's all my fault." Holly finally snapped, leaning against Artemis for support.
"It's all my fault. If I hadn't messed up so many times he wouldn't have come with me. And then he wouldn't be dead." She sobbed, over and over, tears leaking out of her eyes since his death.
"Shhh. It will be okay." Artemis tried to console her, until finally, her sobs died down.
"I'm sorry." She whispered, whiping her eyes.
"It's okay. Come on. The others are waiting for us." Artemis whispered, staring into her eyes. One blue on Hazel. The eyes were murdered on each face, both with the same colored eye.
"I'm sorry I lied to you." He said, before taking a needle and stabbing it into the fairy's neck, injecting the knockout serum. Resulting crashes from around the shuttle indicated all of the other magical beings going down as well.
"Sorry. Did I go to early?" Butler poked his head in, but his voice was wrong. And his size. And weight. Butler suddenly pulled back his facing, showing a pixie- who now looked human- baring her teeth at Artemis Fowl.
"Nobody noticed anything until thay stupid dwarf said something about my height. I was only a few inches behind. I can't make the stilts taller!" Opal Koboi fumed.
"It's okay. Help me take them back to headquarters, with Root." Artemis said, his eyes dark and pupils dilated.
Something wasn't right.