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It's a quiet time in the Halo universe. The war with the alien Covenant is over (we won), there's a massive artificial planet (Onyx) for the Office of Navy Intelligence to play with and exploit Forerunner technology, and Earth's space going really-big-stick, the Infinity, is just about ready for operations.

Dr. Katherine Halsey, the woman who engineered the Spartan super-soldier program that resulted in Halo's game character, Master Chief, as well as all the exoskeleton clad warriors, is being held under a sort of working house arrest because her methods fall short of ethical, including child napping and human experimentation.  As she points out in the prologue for Halo 4, the video game that covers approximately the same period, humanity owes its continued existence to her work, but with the war over, people tend to get picky about ethics. In Halo: The Thursday War, it turns out that this might not be quite the right time to get all that picky.

Product Description: Welcome to humanity's new war: silent, high stakes, and unseen. This is a life-or-death mission for ONI's black-ops team, Kilo-Five, which is tasked with preventing the ruthless Elites, once the military leaders of the Covenant, from regrouping and threatening humankind again. What began as a routine dirty-tricks operation -- keeping the Elites busy with their own insurrection -- turns into a desperate bid to extract one member of Kilo-Five from the seething heart of an alien civil war. But troubles never come singly for Kilo-Five. Colonial terrorism is once again surfacing on one of the worlds that survived the war against the Covenant, and the man behind it is much more than just a name to Spartan-010. Meanwhile, the treasure trove of Forerunner technology recovered from the shield world of Onyx is being put to work while a kidnapped Elite plots vengeance on the humans he fears will bring his people to the brink of destruction.

(Source: Tor Books)