A/N: See Chapter 1 for Disclaimer.

Chapter 2: The Doctor's Prayer

Over the next month, the Doctor continued to struggle with himself inside. He'd gone through a similar struggle years before when both Ensign Harry Kim and Ensign Ahni Jetal were badly wounded by a mysterious alien while on an away mission. They were dying, and the Doctor only had enough time to treat one patient. In such circumstances, he was programmed to treat the patient who had the higher chance of survival. However, his program determined that the two ensigns had an equal chance of survival. Much like his situation aboard the Idora, time was of the essence, and he had to act fast. As difficult as it was, he had to choose one patient over the other before both of them were lost. He chose to treat Ensign Kim, the patient he was closer to, and his choice caused a conflict in his programming that he had to struggle to work through. The Doctor had needlessly blamed himself for Ensign Jetal's death, but as the years passed, he came to realize that it truly wasn't his fault that he'd ended up in that tragic situation. He never beamed over to another person's ship and fired a terrible weapon at two innocent people; the alien did that. And it wasn't the Doctor's fault that he was the only one on Voyager with enough medical expertise to perform the required surgery to save their lives and that a choice had to be made. Furthermore, as awful as it was to have to choose to treat one patient over another, in the end, it was a better outcome than simply doing nothing and losing both of them, and the Doctor eventually recognized that.

However, this situation was a whole other ballgame. The Doctor had no direct responsibility in the injuries that Ensign Kim and Ensign Jetal sustained and he was clearly not to blame for the fact that he had to choose one patient over the other. But this time, he played an active role in the ending of two innocent lives, and there was no escaping that knowledge. He made the decision for Dr. Giala and Dr. Tress to beam them over to a hostile Piran ship, captained by a madman who was hellbent on murdering them to get revenge. He knowingly sent them to their deaths without giving them any say in the matter. He became the judge, jury, and executioner of two kindhearted, brilliant women who still had many years of life ahead of them. He willfully made this ruthless decision to end their lives in cold blood. He knew he may as well have killed them both with his own hands, and it was destroying him on the inside. The Doctor didn't know who he was anymore.

During the four weeks that followed the Doctor's life-changing experience aboard the Idora, he came to the end of himself. He knew that he had a terrible stain on him that he couldn't clean up on his own. Ordinarily, the Doctor was the last one to even consider a belief in God, but these weren't ordinary times. He knew, down to the very depths of him, that he needed something that only a force outside of himself, greater than himself, could provide. He needed forgiveness. He needed the horrific thing he'd done to somehow be wiped clean.

He wasn't entirely sure what it was he was searching for when he began doing extensive research into all the various religious beliefs humanity had held over the centuries. He just knew that even though he had always looked down on people who believed in God in the past, seeing them as weak and primitive, now, there was something within him that desperately needed God to exist. But despite the fact that he was doing thorough research into humanity's various religions as well as the Bajoran and Klingon religions, he knew instinctively that he wasn't searching for religion. He was searching for something much greater than religion. He was searching for the Truth.

Finally, and reluctantly, he began searching in one last place: the Bible. After reading hundreds of texts that different religions considered sacred, he began studying Scripture. In human culture today, Christianity was typically viewed with contempt, and the Doctor was no exception. He too believed that Christians in the past were intolerant bigots and that Christianity's claim that Jesus Christ was the one and only way to God the Father and an eternity in heaven was horribly arrogant. But the more he studied the Bible, the more he came to realize that there was a stark difference between Christianity and all other religions. Every other religion he'd studied was, in a nutshell, man's attempts to earn his own eternal salvation. It was Christianity that acknowledged that no imperfect, sinful human being could ever attain God's standard of perfection on his own; that was all about nothing except pure, simple faith in the Son of God to achieve for man what man could never hope to achieve for himself. The Doctor knew earning his own salvation could never work for him because no amount of good deeds could ever undo his cruel command decision and restore the lives of the two innocent women he sent to their deaths. Only a perfect Being who was far more powerful than he was could find a way to heal the damage he had done and give him the forgiveness he needed so badly.

One evening at the end of his shift, the Doctor was in Holodeck Two running a program of a beach house in Hawaii. He stood on the front porch and watched the sun setting over the ocean. It was truly a gorgeous sight, but it just wasn't the same as the real thing. The Doctor had been on a number of worlds in the Delta Quadrant during away missions and he'd seen actual sunsets, and real, live sunsets seemed to be so much more magical than anything a holodeck could produce. He knew that if the beautiful and miraculous galaxy they'd been exploring for so long really had been created by Someone and had not been a random accident, then that Someone was terrifyingly powerful. Terrifyingly holy. Deserving of nothing but the deepest reverence and respect.

The Doctor eventually left the front porch and walked down to the beach. There were no other holographic characters hanging around in this program, so the Doctor was truly alone with his thoughts. After walking along the beach for a little while, finally, he looked up towards a God that he had once refused to believe in. That he now hoped existed because he knew he desperately needed Him.

The Doctor sighed then, and finally, he told the Lord, "I don't know what to say. I don't know where to begin. For all of my holographic existence, I've believed that it was primitive and foolish to believe in You. Maybe it still is; I don't know. But if You are there…if You even listen to holograms…then I really need Your help. If You do exist, I wouldn't blame You if You did find a way to eventually send my holo-matrix to hell. I deserve it after what I've done. But if You have room in Your heart for a murderous hologram, then please, have mercy on me, Jesus," he whispered as tears freely flowed from his eyes. "If You can go to the cross to make it possible for the sins of human beings to be forgiven, please let there be forgiveness for me, too. Please forgive me for killing Dr. Giala and Dr. Tress in cold blood. Please forgive me for every sinful thing I've ever done or ever will do. Help me. Please."

In the next moment, the Doctor literally felt Someone breathe life into him. And all of the sudden, he felt a heart, a human heart, beating in his chest. Then he heard a still, small whisper, telling him, "Your sins are forgiven."

Tears of overwhelming relief flowed from the Doctor's eyes for several minutes and he knew beyond a doubt that he'd been reborn. He knew that he wasn't imagining any of this; that it was real.

When the Doctor was finally able to talk again, he said, "Computer, give me a medical tricorder." Immediately, one appeared before his feet and he bent down and picked it up, and then he held it in front of himself and examined himself. When he saw the readings, he was stunned. The tricorder was picking up life-signs from the Doctor. He had a temperature, a blood pressure, a heartbeat. He was breathing real air into and out of his lungs. As astonishing as it was, the Doctor was now a human being.