In general, it starts in the 'More or less' present. Then, after they leave the monastery, there is a scene where they hide in the trees for a moment, as a heavenly vehicle passes.. From there, you go back to Sam's history, basically remembering how things got to where they are now. After that, they return to 'now' for the finale.
To break it down a bit more:
Yama calls Sam back from the Golden Cloud. How he got there, you will find out in the next segment. Mara comes to investigate. They leave the monastery, and the 'flashback' segment begins.'
The flashback begins: Prince Siddhartha (Sam, again), as on old man comes to town, to discover things have changed mightily. He decides to oppose the order of things, ransacks a temple (acquiring things he will need in the process) and vanishes to start the next step.
The rise of the Buddah; still in the 'past', Sam takes on the role of the Buddah, and forms a one-man antithesis to the Gods. This eventually leads him to a confrontation with Yama, and to leave for Hellwell, to get some 'specialized weaponry'. Eventually (I'm trying not to spoil the how/why here), he is taken back to the city of the gods, and eventually ends up in the Golden Cloud, from whence he was brought back at the beginning of the book.
Back to the Present: Sam is back, and things have changed in many ways due to his earlier actions. He returns to his fight, and the climax of the story occurs. In many way it parallels his earlier battles, but with different results.
I'm doing this from memory, but it should give you an overview -- I tried to leave major plot points out, but this should give you a roadmap of the path of the book.