In a genre noted for epic scope and lengthy timelines _Genesis_ by Poul Anderson really stands out. A billion years passes in the course of the novel though as one might imagine the reader does not follow along all or even most of what transpires in this setting's history.
Reminding me in some ways of another excellent novel of his, _Starfarers_, Anderson handles the huge sweep of time in the book in several ways. For many of the individuals involved, they are traveling near the speed of light and relativistic effects mean that a few years for them translates into tens of thousands of years for the outside universe.
A second way the author deals with such vast timelines is a plot device he used also in _Starfarers_; vignettes. In both books, Anderson would illustrate how human culture and history has progressed over huge amounts of time with what were basically short stories, portraits of humanity at a given place and time along the novel's continuum and as in _Starfarers_ tied in with the one of the novel's main themes.
There was a third way the billion-year time frame was handled. Unlike in _Starfarers_ most of the main characters aren't human, they were either originally human and had their memory and personality uploaded into a machine consciousness or were artificial intelligences to start with. In this setting, actual physical human beings are too fragile and too expensive to travel the stars themselves, and instead uploaded humans and artificial intelligences make the journey instead (a similar concept used in the excellent trilogy by Sean Williams and Shane Dix that began with the novel _Echoes of Earth_).
Though the novel begins in the relative near future, the main character being the astronaut Christian Brannock, busy with exploring the planet Mercury and an early pioneer of working in close partnership with a robotic artificial intelligence, the majority of the novel takes place in the far future, the results of such pioneers as Brannock and others. After a series of vignettes that show the progression of human history on Earth with the rise of increasingly powerful (and dominant) artificial intelligences, most of the novel is set in the far, far future. The artificial intelligence that controls Earth, named Gaia, has been strangely silent in the vast community of artificial intelligences that spans the entire galaxy and one of these artificial intelligences dispatches an emissary along with a downloaded human consciousness - the original Christian Brannock, one of the first people ever uploaded - to explore what is going in the birthplace of all galactic civilization. Additionally, it would seem that the Earth's biosphere is failing and the galactic network of intelligences wants to know what Gaia proposes to do about that, though again, Gaia is nearly silent on the matter. What will the emissary (named Wayfarer) and Brannock find? What was Gaia hiding? Does Gaia have some sort of sinister plan or is it just something the galactic community cannot understand unless one of its own sees for itself?
A major theme explored in the novel is the nature of free will. As the machine intelligences through the course of a billion years become more powerful, intelligent, capable, and responsible for more and more details of life on Earth, is that a good thing for all concerned? Is the prevention of suffering, chaos, and evil always in the best interest of humanity? To get the good in humanity - friendship, charity, artistry, courage, leadership, love - does one have to allow for the bad - suffering, selfishness, greed, cowardice, and tyranny? The machine intelligences have achieved a great deal, a truly impressive body of knowledge and a civilization that is already spreading to nearby galaxies, but what have they lost in this pursuit?
As is it hard to have a novel where the protagonists have knowledge far above and beyond any human is capable of, usefully the novel is presented largely through the eyes of the various human characters. In the far future setting the main characters are the intelligence and personality of Christian Brannock and a downloaded intelligence that Gaia provides to interact with him, a woman by the name of Laurinda Ashcroft.