Halo: The Fall of Reach takes place in Master Chief's,
or John's, past. It starts off with the beginning of the entire
SPARTAN project, talks about all the Spartan's and their missions, the MJOLNIR armor, and (obviously) the fall of Reach, the human's main defense
planet before Earth. It leaves off right before the game Halo:
Combat Evolved begins with the actual discovery of Halo.
Halo: The Flood takes place exactly where the The Fall of
Reach ends, or, where the game begins. This book essentially fills in
the details of the Halo story line you don't get to hear about in the game.
The game tells you Master Chief's story, and the book tells you everything
else. It ends at the end of the game with John and Cortana aboard the
Halo: First Strike is the latest addition to the Halo book series. It
picks up the story after the game and takes to many different places.
I don't want to ruin any of the book, but basically Chief and a few close,
personal friends of his find out that the Covenant are planning a massive
assault on Earth (a la Halo 2) after they learn of it's whereabouts.
They are all gathering at one location before they move en masse.
Chief decides to kick it to the Covenant and delay their assault on Earth by
going on a deadly "First Strike".