Anyway here's a rundown of the two books (http://en.wikipedia.org/wiki/Commonwealth_Saga)
The Saga begins in 2380, the human race has had wormhole technology for over 300 years thanks to the work of Nigel Sheldon and Ozzie Isaacs, and has colonized several hundred planets across hundreds of light years. On a distant planet, Astronomer Dudley Bose performs the first detailed observations of an astronomical event known as the Dyson Pair Enclosure. Two stars, located roughly 1,000 light years from Earth (750 light years from the edge of Commonwealth space), seemingly disappeared some time earlier. The theory is that they have been enclosed inside Dyson spheres.
Bose's investigations reveal that the enclosing of Dyson Alpha and Dyson Beta (as the stars become known) occurred quickly and simultaneously. These facts mean that the technology of the Dyson aliens, or possibly other unknown aliens, surpasses that of the Commonwealth; furthermore, did the Dyson Aliens enclose themselves, or did some other force enclose them? Was it for protection or to protect those outside the spheres? To investigate, the Commonwealth builds its first interstellar ship, the Second Chance. Commanded by Wilson Kime, one of the first men to walk on Mars, using a self-generating wormhole for propulsion, the Second Chance travels to Dyson Alpha.
As they arrive and begin to explore what appears to be an enclosure generator, it is shut down by an unknown mechanism and the barrier around the star disappears. Inside the first imprisoned star system is an incredibly warlike and aggressive species, a race that come to be called the Primes. They consist of intelligent immotiles that breed and control vast armies of sub-sentient 'motiles' via electronically extended neural interfaces. The few immotiles constantly vie with each other for territories and resources.
Primes had colonized Dyson Beta and enslaved its native inhabitants in the process. Beta's Primes started to routinely alter themselves through genetic manipulation and mechanical augmentation and therefore were referred to as alienPrimes by the Alpha Primes. They also broke away from the control of Alpha's Primes and thus a war began between two systems. The war continued until the barrier was erected around the stars.
After capturing two crew members of the Second Chance, one of whom was Dudley Bose, the Primes eventually discover the location of the Commonwealth. Upon learning of the Commonwealth's existence, the dominant immotile grouping, MorningLightMountain, makes it its primary objective to destroy the Commonwealth. MorningLightMountain believes that it is necessary to eliminate all other life in the Universe in order to secure its survival into the distant future, because it views all life that is not under its control as a potential threat.
Following the capture of the two crewmembers, MorningLightMountain discovers the concept of wormhole technology, and quickly creates its own generator. Using wormholes to transport and detonate nuclear weapons within the defenses of other immotiles, it secures its dominance over the Dyson Alpha solar system by becoming the only surviving sentient member of its species.
At the same time, an underground human organization known as the Guardians of Selfhood is determined to prove the existence of an alien known as the Starflyer, which originated in the crash of an ancient spacecraft (the Marie Celeste) on the planet Far Away. The Guardians of Selfhood have been declared a terrorist organization by the Commonwealth's government, and are pursued by famed investigator Paula Myo, working on behalf of the Commonwealth government. Throughout both books, Ms. Myo becomes gradually convinced that the Starflyer may be real and has organized the liberation of the hostile aliens for its own purposes.
The Prime attack on the Commonwealth is devastating, including widespread use of nuclear weapons to both subjugate and contaminate the human worlds, resulting in tens of millions of human deaths.
Judas Unchained, the second part of the Commonwealth Saga, picks up where Pandora's Star's abrupt ending left off.
The story begins with the small human resistance that exists on what remains of the Commonwealth worlds attacked by the Primes. Human resistance forces have found two ways to fight back: using the Prime weapons (primarily directed-energy weapons) against the invaders, and disrupting communication between the slave caste (motiles) and the commanding caste (immotiles) of the Primes. Meanwhile, the humans in the remaining Commonwealth pursue other plans: to develop a set of weapons and warships to defend against the next Prime invasion and force the conflict back into Prime space; to develop a "quantumbuster superweapon" based on technology supplied, unbeknownst to most humans, by the Starflyer; and to prepare for the evacuation of known space altogether if necessary.
Eventually, the human forces decide that there can be no other solution to the conflict than to commit genocide and destroy the Primes entirely. However, it is revealed that the Primes are planning a much larger invasion, which humanity will be all but powerless to stop.
As the war rages, the human forces begin to build much faster, better armed, ships and fitting them with new "quantumbuster" weapons. These weapons function by converting the entire rest mass of an object into energy, and are thus capable of destroying an entire planet. Later on, a more advanced quantumbuster is deployed, which is capable of inducing a main-sequence star to go nova via a feedback loop where the energy from the conversion is used to further expand the radius of the effect field. Despite the original plan to use it on the Dyson Alpha star and thus kill the entire prime race, a modified field version of a normal quantumbuster is eventually deployed on the Dyson Alpha forcefield generator, destroying the mechanism that was interfering with the generator's systems. This allows the mechanism to reactivate, trapping the Prime aliens inside and avoiding genocide.
Meanwhile, it has emerged that the Starflyer is in fact an AlienPrime which, by chance, escaped the enclosure event. The human forces engage in a desperate chase to prevent the Starflyer from escaping the Commonwealth. After defeating the Starflyer's army and encircling the Marie Celeste, The Guardians of Selfhood destroy the Starflyer with a massive directed hurricane, freeing humanity from its thrall.