After reaching Falmouth on October 2, 1836, Darwin rushed home to Shrewsbury to see his family. He arrived late in the evening and snuck into his room to sleep for the night. In the morning his family was shocked and pleased when he joined them for breakfast. He was five years older and a few pounds lighter than when he had left.
He was also much more driven. When he left on the Beagle it was in part because he had no direction, and certainly no enthusiasm for the prospect of entering the Church. When he returned, he was a certified naturalist. He rapidly gained memberships in the Geological Association, the Geographical Association, and the Zoological Association, and he set about getting all of his notes and samples ready for analysis and publication. He and FitzRoy were both preparing accounts of the voyage of the Beagle, to be published together. Darwin's would focus on his observations as a naturalist and FitzRoy's would focus on his adventures as captain. Darwin spent most of his time in London, the center of scientific expertise; he needed as much help as he could to decipher the thousands of species and samples he had brought back with him. He farmed out his samples to the people he most trusted. He treated some of the as colleagues, lending the sample in exchange for their advice on what to do with them; others he treated as employees, paying them with his father's money.
Although entering the Church had been a vague possibility before the Beagle, it was now out of the question. Charles began to look for a way to set himself up as a gentleman-naturalist. He also started looking for a wife. After some debate, recorded in his notes, he decided that marriage would suit him better than bachelorhood. He chose his cousin, Emma Wedgwood, whom he had seen for so many years on his hunting trips to Maer, proposing to her in November 1838. Emma happily accepted and they were married a few months later, in January 1839. Their first house was nothing spectacular: a small place on Gower St. in Bloomsbury. It was close to the scientific community but also, unfortunately, to the dirt and noise of industrial London.
It was at about this time that Charles's health started to fail. Soon after the birth of his first son, William, in December of 1939, Darwin found himself becoming nauseous and weak, suffering from pain and insomnia. Doctors, including Darwin's father, could find no concrete problems to treat, so he was left to suffer on his own. His sickness plagued him throughout his life, though it grew somewhat less noxious in his later years. Emma devoted herself to taking care of him in his weak moments, of which there were many. In 1842, to escape the din of London, Charles and Emma moved to the village of Downe in Kent, where they took up occupancy in the Down House. Down was a quiet, out of the way place where Darwin could focus on his science, nurse his increasingly poor health, and avoid the tribulations of London society.
At the Down House, Charles and Emma settled down into a routine that would last a lifetime. Emma took care of the house, the finances, and Charles's health. For Charles the day consisted of reading and working with specimens in the morning, lunch with Emma, walks around the grounds and correspondence in the afternoon, then dinner and tea, perhaps followed a game of backgammon with Emma. Then Emma might read bits of a novel to Charles before sleeping. After William's birth in 1839 came Annie, in March 1841, and eventually eight more children between 1842 and 1856.
In 1837, Darwin started keeping notes on evolution, although he would not publish anything on the matter for another twenty years. In 1842, he made a first sketch of a theory that included the core idea of his theory of evolution: that species descended from each other with modification due to natural selection. In 1844 he expanded the sketch into a 189-page manuscript, but he was still not ready to publish. He felt unsure of his speculations and afraid of the repercussions in the scientific community. Having established his reputation with careful observation and clear, direct reporting, he trembled at the thought of going as far out on a limb as a theory of evolution would take him. So he kept his theory to himself and waited until he thought he could make a waterproof case for it.
In 1842, Darwin published The Structure and Distribution of Coral Reefs, a detail-heavy, carefully written account of the reefs he had observed in the Pacific and Indian Oceans. By 1846, he had published all that he would on the voyage of the Beagle, including his journal, the book on coral, another on volcanic islands, and various papers.