A/N: This story is based on the television series, Star Trek: Voyager, which as far as I know is the property of Paramount Pictures. No infringement is intended.

Chapter 1: Beloved Physician

Six weeks ago, the former Emergency Medical Hologram of the starship Voyager made an appeal to the Creator of the universe, and He answered in a big way. After praying to Christ for forgiveness of all his sins, most notably the brutal command decision he had to make resulting in the deaths of two innocent Nali doctors, he felt the Lord, Himself personally breathe new life into him, and he was transformed into a human being. He became a living being for the first time.

When Captain Janeway and the rest of the Voyager crew learned of the Doctor's transformation, they were stunned to say the least. They were especially shocked when he explained to all of them that he only became human after he chose to put his trust in Jesus Christ. Captain Janeway immediately checked the ship's computer and sure enough, all files pertaining to Voyager's Emergency Medical Hologram were gone and the EMH could not be activated. She ordered Tom Paris to perform a thorough examination on the Doctor, and when he did, it was determined that his DNA was identical to that of Dr. Lewis Zimmerman, the man who created his holo-matrix. It was almost as if the Doctor were now Zimmerman's identical twin brother. The Doctor still had all the memories of his experiences during his life on Voyager and in many ways, he was still the same loveable egotistical hothead he'd always been. In other ways, though, he was deeply and profoundly changed, and it took a little time for both the Doctor and the crew to get used to it.

At Captain Janeway's direction, the crew conducted sensor sweeps of the area and they went over every square millimeter of both holodecks with a fine tooth comb, and they found no evidence of any kind of alien life or spatial anomalies or anything that could possibly explain the Doctor's transformation. Captain Janeway and the crew kept Voyager in its current position for the next several days, halfway expecting that Q would show up and let everyone know that it was he who'd made the Doctor human just to mess with him. But that never happened. Captain Janeway even spoke with the Doctor about his experience in the presence of Tuvok, who telepathically read the Doctor's mind during the conversation. Although Tuvok wasn't an empath, both his telepathy and all his years of experience working in Starfleet security told him that the Doctor was, in fact, being fully truthful about what had happened to him. Finally, even someone like Captain Janeway, who had been raised from birth to look at everything with a skeptical scientist's eye, had to accept that the Doctor was telling the truth about his sudden transformation and that some kind of greater power out there did in fact hear the Doctor's prayer and make him human. She wasn't willing to concede that that power was definitely Jesus Christ, but at the same time, she was willing to be respectful of the Doctor's spiritual beliefs, just as she would be with any other member of her crew.

Not long after the Captain made her peace with the Doctor's situation, two important changes transpired for the crew. First of all, Neelix rejoined the crew with his new family. The asteroid that Mr. Neelix had been living on with his new wife Dexa and his stepson Brax was suddenly targeted by two Borg cubes. Thankfully, a very large Nali ship was in the area and they answered the distress call Oxilon sent out. They helped Oxilon and Neelix gather up the five hundred Talaxians there and get them on the Nali ship, and the Nali ship quickly departed the asteroid before the Borg arrived. The Nali ship soon caught up to Voyager, and Captain Janeway was more than happy to receive Neelix back into the fold, along with Dexa and young Brax, while the Nali kindly offered to allow Oxilon and the other Talaxians to remain with them and become a part of their (already large) crew.

The second change that happened was something that the Voyager crew had been looking forward to for a long time now, Ensign Kim in particular. Because Voyager only had a crew of about one hundred and fifty people, there was no room for any real advancement in rank. However, since Voyager had been in two-way contact with Earth for quite some time now, Captain Janeway had long since made her wishes known to Starfleet Command to be able to give promotions to deserving members of her crew. It took the pencil-pushing, out-of-touch bureaucrats at Starfleet Command long enough, but they finally approved the Captain's request to bend the rules and allow her officers to advance in rank accordingly. Almost all of Captain Janeway's crew were promoted two ranks above their current one. Lieutenants Paris and Torres each became Lieutenant-Commanders, and thankfully, finally, at long, long, long last, Ensign Harry Kim was promoted to the rank of full Lieutenant.

Other changes happened soon after everyone got promoted. Neelix's new wife Dexa was a nurse practitioner, and she was anxious to serve aboard Voyager and give the Doctor and Tom a hand in Sick Bay. After getting to know Dexa a little better, Captain Janeway soon came to like and admire her, and she decided to grant the Talaxian woman a field commission. As a trained nurse, Dexa had to start out at the rank of ensign like all nurses in Starfleet, but it was likely that after a year of service, she would be allowed to advance to the rank of Lieutenant Junior Grade like any other Starfleet officer. And since she was already a Talaxian nurse practitioner, the Doctor was certain that after another year of extensive instruction and training, Dexa could become a doctor in her own right. Dexa was very excited to become the Doctor's student and she very much looked forward to completing her medical training and becoming a Starfleet physician.

And there was a change in store for the Doctor as well. It took a good deal of arguing with Starfleet Command, but even though it had been difficult, Captain Janeway did manage to get her way in the end as she almost always did. (It sure didn't hurt to be on a first-name basis with a number of decorated Starfleet admirals!) Now that Starfleet Command agreed to her request, all that was left was for Captain Janeway to inform the Doctor. And for the Doctor to finally make an important decision.

Captain Janeway met the Doctor for lunch on Holodeck Two to inform him of the good news she had for him. Four months ago, after having been imprisoned by the Hierarchy aliens and being rescued, they'd begun having coffee together on the holodeck. During their coffee sessions, they always ran a program of a lovely sidewalk café in Buenos Aires that the Captain had always liked, and they were running that program today. They'd gone there for coffee quite a few times over the past few months, and in that time, they truly had started growing closer. Now that the Doctor was human, he no longer had to settle for the holographic illusion of drinking coffee with Captain Janeway. Now, he was able to have a real cup of coffee with her, and he was finally able to enjoy the pleasures of eating food, something he had desired for a long time. Captain Janeway wolfed down her lunch because she was so anxious to tell the Doctor her news, but the Doctor, new to food, took his sweet time, savoring every bite of the huge salad he'd ordered. Thankfully, the Captain was a patient woman and while she was anxious to talk to the Doctor, she could hardly blame him for enjoying his food so.

When the Doctor finally finished his last bite of food, Captain Janeway chuckled a bit, and she asked him with a smile, "You enjoyed that, didn't you?"

"I certainly did, Captain. Becoming human has opened up a whole new world to me. Now I finally know how it feels to enjoy a meal. To smell a pleasing aroma. To feel tired and experience the restfulness of sleep. To stub my toe. It's given me a whole new perspective."

"Well, while we're on the subject of your humanity, I've been talking some things over with Starfleet Command. Although they all find your story questionable, no one can deny the results of the examination Mr. Paris performed. You are, undoubtedly, a human being now. And it's clear that you still have all the memories of the past seven years intact. Your status as a person has always been in question as far as Starfleet is concerned, but that status can't be questioned any longer. You are a person now, and not even Starfleet Command can deny that fact. I got into some arguments about it with Starfleet Command, but I put my foot down and I insisted that Starfleet acknowledge your personhood and grant you the rank you deserve. They…reluctantly…agreed that it was time for you to finally be granted your own commission." The instant the Captain said that, the Doctor's face lit up like a Christmas tree. "All doctors in Starfleet start out with the rank of Lieutenant Junior Grade," she continued, "but I felt that given your past seven years of experience aboard Voyager, you deserved to be promoted two ranks just like most of the crew have been. I couldn't get Starfleet Command to go as far as to grant you the rank of Lieutenant-Commander, unfortunately. However, I did get them to agree to grant you the rank of full Lieutenant."

"I…I don't know what to say," the Doctor gasped, overcome with emotion. "I'm honored that you did all of this for me, Captain. Thank you."

"You deserve this, Doctor," Captain Janeway told him with a big smile, and although the Doctor smiled in return, the Captain was almost convinced that he was on the brink of tears. A few moments later, she said, "Now on to the next order of business. Simply addressing you as 'Doctor' isn't going to cut it anymore. Now that you officially have your own Starfleet commission, you need to have a name."

"I've been trying to find the right name for the past seven years without any success. I'm certainly open to suggestions if you have any."

"As a matter of fact, I do have one name in mind."

"I'm all ears. What is it?"

"Luke."

"Luke," said the Doctor, trying the name on for size.

"Given your newfound Christian faith, plus the history of the name Luke, it seems appropriate. After all, Luke was thought of as 'the beloved physician' in the days of the early Christian church. And here on Voyager, you're our beloved physician."

"Thank you so much for saying that," the Doctor told her in an emotional whisper. "It means a great deal to me to know you feel that way. It really does."

"Well then, let's make this official," said the Captain as she rose from her seat, and the Doctor stood as well. In the next moment, she bent down and pulled out a small black box she'd kept hidden underneath the table. When she opened the box, the Doctor saw two silver round pips, and he smiled. She then said, "Dr. Luke…wait. What about a last name? Zimmerman, perhaps?"

The Doctor shook his head. "I don't see much need for a last name, Captain. I'm more than happy to simply be known around here as Dr. Luke. Your beloved physician," he said rather smugly, and the Captain barely suppressed a chuckle.

"Very well. Dr. Luke, you are hereby granted a commission of Lieutenant." A couple of seconds later, Captain Janeway pinned the two silver pips on Dr. Luke's collar. "Congratulations."

"Thank you, Captain," Dr. Luke whispered while she gave his hand an affectionate squeeze. Deep down he really wanted to reach out and give her a big hug to express his gratitude for all her efforts on his behalf, but he decided against it. Even though they were closer now, she was still his captain and like all officers under her command, he had to maintain a certain distance. He knew he had to remain respectful and maintain a certain level of professionalism with her at all times, even on the holodeck. The last thing he wanted was to make the Captain feel uncomfortable after everything she'd done for him.

"You're very welcome," she said with a kind smile. Several long moments later, she told him, "Well, I'd better get back to the Bridge."

"Yes, I should be getting back to Sick Bay as well."

"I'll see you at our next coffee session."

"Aye, Captain," Dr. Luke said with a nod, and then both he and Captain Janeway exited the holodeck together.