Krelian
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Here, it gets a little blurry. During their time together, Sophia managed to get through Krelian's walls and bring him out into the open. She suggested he read instead of giving in to his anger, and that led to his interest in Melchoir's experiments later on. While he served as a high-ranking member of the clergy, he also spent time assisting in the translation of ancient documents found in the ruins of Zeboim. He and Melchoir were able to make great advances. But these discoveries (at least in Krelian's mind) were always made in the name of Sophia, not for the sake of scientific thought. By this time, Krelian was completely in love with her.
When the war between Nisan and Solaris started, Krelian was given command of the Nisan Army and the title of Holy General*, and he led the Kahal, a small group dedicated to protecting Sophia from harm. Other members of this group included Roni and Rene Fatima and later, Lacan. Shevat allied with Nisan, and thus began Krelian's scientific studies.
As far as I know, Lacan didn't join up until later. He had met Sophia in the past, but did not linger with her as Krelian did. When he showed up again and started drawing Sophia's attention, it created the most infamous love triangle in the game's long history. Krelian loved Sophia, but he knew that she didn't return his feelings - she loved Lacan. The painter, of course, didn't realize any of this. Krelian stepped aside so Sophia could be free to love the one she desired, but Lacan refused to notice, and that angered Krelian to no end. It's very possible the animosity between them (at least in Krelian's books) stems from this situation.
It can be argued that Krelian's love for Sophia wasn't romantic, so much as worshipful, and maybe a product of his wish for a mother figure. She is the 'Mother'. I think she took on that role during their seven years together, and he seems to look up to her like that. A few of the Japanese pages I've been to in the past have talked about this, but it's all up to interpretation.
When Sophia sacrificed herself to save her army, Krelian's faith was shattered. His prayers were left unanswered, and he came to the conclusion that god must be dead, or just nonexistent altogether. He stayed with Roni and Nisan until the end of the Diablos Conflict and then left to wander the world in search of a way to fulfill his promise to create a god with his own hands. He met Miang on this long journey, maybe more than once (the PW is purposely vague), and when she promised to help him achieve his goal, he followed her to Solaris to pledge his loyalty to Cain. The book says he came into contact with Cain before Miang, but its previous statement makes me think he just didn't know who/what she was before he made his promise to the Emperor.
Miang revealed the truth of everything to Krelian - Deus, Zohar, Lacan and Elly, and her own purpose. With this knowledge, his goal was more clear-cut than before, and if his faith wasn't quite dead, it certainly died the day she told him what was really going on.
Krelian merged his own knowledge, Kim's notes, and Solaris's technology to sustain Cain's life and revivie the Gazel Ministers (probably at Miang's prompting); he used the same knowledge to extend his own life, and 'punish' Zephyr and her advisors by extending theirs as well, hoping to cut them off from the rest of the world. It's implied that he holds the key to their continued existence - if he gets tired of them, he can end their lives at any time. (I'd really hate to be Zephyr.)
With this preparation, Krelian started Project Noah, his effort to revive Deus. He released the Limiters against Shevat and the surface population and continued his work with nanomachines. He left the Contact and Anti-Type to Miang, at least until he got tired of waiting and decided to create Ramsus. The Ethos was probably his idea for conducting the M Project (Soylent, memory cubes, etc.), but it was also an extention of his plan to resurrect god.
It almost seems like Krelian's faith never really broke at all, sometimes, but transformed into a quest to find the true god that he knew must exist somewhere. He despised the Gazel for their arrogant attempt to become that ideal. His desire to create god became a desire to become one with god, and (according to the PW) when he touched the Raziel Computer for the first time, he touched the mind of this god he had been searching for. The knowledge he gained of Zohar's purpose spurred him on in his efforts to revive Deus, but I think he also had a complete change of heart. Despite what he says to Fei during the last battle, his speech has the feeling of someone resigned to being wrong. Unfortunately, Krelian had progressed too far into his plans, and there was no turning back.
Krelian's ultimate fate can be learned by playing Xenogears. I know this profile is missing nearly everything that happened during the game, but... well, you can play the game for that! His profile consists mainly of what was said in the Perfect Works, and that didn't cover the entire game storyline either. ^.^ More information can be found in the History section and character profiles for characters like Sophia, Lacan, and others related to his story in the game.
* We had difficulty coming up with a precise translation of Krelian's rank in the Nisan army. 'Holy General' was the closest approximation we could come up with at the time.