Disclaimer: I do not own Star Trek or any of its characters.

Please refer to the Author's notes in Chapter 1.

Thank you to Just a Crazy-Man, Obsessive66, AngelQueen, Ataxia O'Rourke, Kushina98, Emberka-2012, royalpinkdogs, Mike, Ace, Zedoc, Saissa, bonesfan4ever, Furionknight, mvaneekhout1 and IrishBug74 for the reviews and all of the readers following this story! Over 10,000 views, I'm very humbled that this story has done so well. I hope you'll enjoy it's continuation, Broken Remnants, which will begin soon.

A/N: I decided that I had to add an Epilogue to this story to bring it up to the new movie. Hope you enjoy!

The Ripple Effect

Epilogue

Leonard McCoy leaned back at his desk and propped his feet up on the desk in Medical on the Enterprise as he looked back at the monitor. "Do you know how long it's been?" he questioned.

Kaitlyn Donovan sat back in her chair and watched his image on her monitor, "Ten months, three weeks, and seventeen hours - not that I'm counting." She shrugged and sighed softly as she sat in the Conference room of the Daystrom.

Leonard's face contorted, "A few months my ass! When will you be coming back to the Enterprise?" he questioned as he tried to contain his gnawing frustration.

Kaitlyn smiled slowly, "Actually, we will be meeting up with you in a month."

Leonard dropped his feet off the desk and leaned closer to the monitor in disbelief, "Are you kidding me? Because if you are, it's not funny!"

"I'm not joking - we got the orders this morning. We are heading back to Earth to switch out some crew, then we will meet up with you and I'll transfer back to the Enterprise." she explained the subspace call she'd received earlier in the morning from Starfleet Command.

Leonard McCoy gave her a small smile - he was ecstatic, but he'd learned over the past ten months not to count your chicks until they've hatched. They'd been promised before of her transfer, and those promises hadn't panned out. He decided to play it safe, "I miss you." he admitted.

Kaitlyn understood his reigned in mood, "I've missed you too, Leonard." She tried to relax, but the events on her ship from the past week had worn on her. "What have you been up to?" she questioned.

"Well, we ran into a real character - his name was Mudd. It was a mess, but we got a small ship out of it." he shrugged. "On that note," Leonard quipped, "what happened that you couldn't call last week?" He watched as she shifted uncomfortably in her seat. "What's wrong with your shoulder again?" He started to get that unsettling feeling again in the pit of his stomach.

"We had a virus sweep through the ship that caused the crew to become violent. I'll transmit Doctor Kor's findings to you as soon as I can." she stated.

Leonard sat stiffly, "Is everyone ok now?"

Kaitlyn shook her head slowly, "No, seven crewmembers died and we have many more injured - that's the reason we're heading back." She looked up as the Conference room door opened.

The young female Yeoman burst in and looked like a deer caught in the headlights, "Captain, Starfleet Command is sending you another Priority message." she said quickly in one breath.

Kaitlyn frowned at the title, "Tell Lieutenant Hotch to patch it through to me in here as soon as I finish this call." she directed.

"But, it's a Priority One message." Yeoman Robins bit her lower lip - shouldn't the Captain answer the call immediately? She was still unsure of the new job she'd been promoted to a few days ago.

"I understand that. There's a door for a reason, and we have a comm system for a reason - you don't have to come running to find me, call me over the comm." Kaitlyn tried to reassure the young woman.

"Yes, Ma'am - I'm sorry that I interrupted you." Yeoman Robins quickly left.

Kaitlyn glanced back at the monitor and frowned, Leonard was looking at her questionably.

"Captain?" he raised an eyebrow.

"Acting Captain - just until Andrew wakes up from his medically induced coma, he had to have a lot of surgery from his injuries." she tried to make the situation not sound as bad as it really was.

"What happened to the First Officer?" Leonard remembered her saying that she never wanted to be a Captain and he wondered how in the hell she'd ended up in the situation.

"He was killed by another member of the crew." Kaitlyn glanced at the monitor as the icon began blinking - indicating the Priority One message on hold, waiting for her to answer. She sighed softly, "It's a long story - and not a pleasant one. I'll send you a message with the findings from Doctor Kor later today - I promise."

Leonard nodded slowly, "I look forward to reading it. Take care of yourself and get another hypo for that shoulder. I'll call you tomorrow after I've had a chance to review Kor's findings." He didn't want to end the conversation, but he knew she had that call from Starfleet Command waiting.

Kaitlyn smiled, "Talk to you tomorrow." She ended the transmission with Leonard and then clicked on the one from Starfleet Command.

XXXXX

Thirty minutes later, Kaitlyn came out of the Conference room and was immediately barraged when she stepped on the Bridge by Yeoman Robins.

The young woman looked at the PADD in her hands, "Ma'am, you have a meeting with Doctor Kor in ten minutes, then at 1100 you have a demonstration in Engineering and at 1300, you have a meeting with the Science Department for an update on the latest subspace scans."

Kaitlyn nodded, "Thank you, Robins. I'll need you to come with me to Medical. Starfleet Command wants an updated list of the crewmembers and the treatment Doctor Kor recommends for them once we get to Earth - I want you to get that list together."

"Yes, Ma'am." Robins quickly acknowledged and followed Kaitlyn into the lift as they headed to Medical.

They entered Medical and headed to Doctor Kor.

The large Klingon had on his white lab coat and looked up from his PADD as they approached. He quickly took note of the way the Captain was walking, "Is your shoulder bothering you again?" he questioned roughly.

"Yes, I just need a hypo." Kaitlyn said as she surveyed the patients in the beds.

"I will decide what you need, Captain." Doctor Kor pointed to an available bio bed for her to get on.

Kaitlyn knew well enough not to argue with the Chief Medical Officer. She got on the bed and waited as he ran the scanner over her. She glanced at Yeoman Robins, "Why don't you get a list of the patients from Nurse Davies." she suggested.

Robins quickly headed to the nurse across the room.

Kor gave her a toothy grin, "Are you tired of your Yeoman already?" he inquired.

Kaitlyn shook her head, "She will do fine, once she gets into a routine. I'm the one who's tired." she admitted.

Kor frowned, "Did you not sleep well?" He clicked his scanner to another option and ran it over her again.

"I've never had the desire to be a Captain of a Starship. It's a lot to undertake when I still have to do my duties as the First Contact Officer. I keep waking up when I remember things that I need to check on." Kaitlyn had grown rather fond of the Klingon doctor - probably because he had a very similar bedside manner to Leonard.

Kor watched her thoughtfully as he closed the scanner, "It is a responsibility to which we elevated you to. This is a unique ship, and in the past ten months you have handled many difficult conflicts between us. You are sleep deprived. Do you have many things to attend to today?"

She shrugged, "Something always needs my attention."

"After you have had dinner, I will give you something to help you sleep tonight. If you don't feel better in the morning, we'll look into some other options." Kor stated, then administered a pain reliever for her shoulder. "Let me take you around to the patients and give you an update on their conditions."

XXXXX

Kaitlyn headed to Engineering and smiled as the turbolift doors opened and Trip Tucker grinned. She stepped in the lift and smiled, "How are you doing Admiral?" she questioned.

"Doing great. I know that Sorek and the Engineering team are anxious to show you their simulated runs of the trans-warp drive." he rocked on his heels in anticipation. The team headed by the Vulcan Chief Engineer had been working for months on the drive.

She glanced at her friend - get him around an engine and he was happy as a lark. She was glad that he'd decided to come on the ship with her, it had given him a focused purpose and helped keep his mind off the loss of Admiral Archer. The two had worked together and been friends for so long. "I'm sure their work is stellar and the simulations will go well. Do you think we're ready to implement it?" she asked as they stepped off the lift and walked to Engineering.

"Sure do." he nodded.

She stopped him before they went through the doors, "Will you be getting off at Earth?" she inquired quietly.

Trip smiled, "Actually, I'll be heading to New Vulcan to stay with T'Mir and her family for awhile."

"I'm happy for you Trip, I hope you have a wonderful time with your family - and you'll get to see Ambassador Spock again." she pointed out.

"It will be good to talk to him again." Trip waved for her to go through the door first.

XXXXX

Three weeks later - U.S.S. Enterprise.

Leonard McCoy pulled himself off the floor when the ship stopped shaking. They had captured John Harrison on Kronos, then he'd revealed his true identity. Leonard clicked on the nearest monitor and waited for the communication to go through. He had to tell her what they'd found out before the Admiral managed to blow the Enterprise up to bits. "Get me Captain Donovan on the Daystrom." he requested.

Kaitlyn's image came on the screen, "Leonard - what's wrong?" she questioned quickly when she saw his expression.

"I think we're in over our heads." he admitted. He quickly explained what had happened and everything they'd learned in the last few hours.

Kaitlyn could feel herself growing angry. She had worked so hard to bring credibility and higher moral standards into the Section when she'd been Director of Operations - and now she found out she'd been duped, tricked, and manipulated by the very organization that she put her name upon years ago. "Leonard, we're still days away - but I'll see what I can do." She was frustrated that there wasn't anything she could do at the moment to help them when their lives were hanging on a thread.

Leonard nodded. He looked up quickly as the ship shook again, when he looked back at the screen, it was black. He closed his eyes tightly and prayed they'd get out of this alive.

Kaitlyn blinked rapidly when the connection was terminated and the screen went black. She quickly thought over their options as she headed back to the Bridge and opened her communicator, "Donovan to Engineering."

"How may I assist you, Captain?" Sorek's calm voice questioned over the communicator.

"Get ready to engage the trans-warp drive." she said as she entered the Bridge. She saw the questioning looks from the Bridge crew.

"Captain, we have not completed all of the trial runs. To engage the trans-warp drive for more than a few hours could potentially do more harm than good to the ship and crew." Sorek stated.

"How much closer to Earth?" she questioned him.

Sorek quickly did the calculations, "We would be there in under four hours."

Kaitlyn frowned, four hours could be three hours too late - but they had to try. "Sorek, prep the drive and get your team ready. Any signs of problems, notify me immediately." she ordered.

"Aye, Captain." Sorek quickly went to work in Engineering.

Kaitlyn walked over to Lieutenant Relch, their Navigator, and stood beside him. "As soon as Engineering gives the go ahead, engage the trans-warp drive and get us to Earth as quick as possible."

Lieutenant Relch nodded, "Yes, Ma'am."

Kaitlyn looked to Commander Tala at her Weapons' post questionably.

Tala nodded in understanding, "All weapons will be ready when we arrive."

Kaitlyn patted the Andorian woman's shoulder, then went and sat down in the Captain's Chair. She took a deep breath and collected her thoughts on what she needed to say to the crew of this very unique ship. She had become well acquainted with all of the crew and felt they trusted her. But one wrong word, one misconstrued connotation in her message and she might have a conflict break out between the species that still didn't completely trust one another. She pushed the button to open the comm system throughout the ship and carefully began to explain the situation they were racing into.

XXXXX

Reviews are greatly appreciated!

I hope you have enjoyed reading The Ripple Effect. The next story, Broken Remnants, will begin soon after Star Trek: Into Darkness is released.