Twain was a Presbyterian, yet for about 4 decades, he made an effort to synthesize his view of human nature and man's relationship to God and the universe. It seems that he was in deep conflict between science and religion. (source: The Bible According to Mark Twain, Introduction by Howard G. Baetzhold)
His writings during those 40 years, reflect the conflict I think he, himself, was struggling with. In Tom Sawyer Abroad (1894), Tom and Huck debated about whether the Sahara Desert was made or just happened. Tom said to Huck, "the trouble about arguments is, they ain't nothing but theories, and theories don't prove nothing, they only give you a place to rest on, a spell, when you are tuckered out butting around and around trying to find out something there ain't no way to find out." Baetzhold believes this paragraph reflects Twain's own thoughts, and I agree.
Like many people who were raised in a particular religion (in his case, Presbyterian), and later as an adult began searching for what they truly believe in because of inconsistencies and doubt throughout their lives, Twain seemed frustrated with what he considered idiosyncrasies of man and God.
For an article I wrote about Twain, I did heavy research that took me days and days -- yet I do not think I even came close to understanding what was really deep within the man's thoughts and heart. I do know that there was something profound and amazing about him -- he fascinates me.
from
Mark Twain Unparalleled:
"Mark Twain was born two weeks after Halley's Comet made it's closest approach to Earth. Like a comet, he lit up the literature world and brightened the hearts of all who loved him and his works. On the night before Twain's death, Halley's Comet again lit up the night sky. The next night, April 21, 1910, Mark Twain left this world -- some say he left as he came into it: on the tail of Halley's Comet.
The Impartial Friend: Death, the only immortal who treats us all alike, whose pity and whose peace and whose refuge are for all--the soiled and the pure, the rich and the poor, the loved and the unloved.- Mark Twain, last written statement"
Twain's thoughts and writings on religion are so vast and deep that I did not attempt to even go there. The best thing for people like me to understand Twain's thoughts and feelings is to read "The Bible According to Mark Twain" (which I have on my
Amazon Wish List) before making a guess on what he really believed.