Pandora's Star is set in the year 2380, or at least that's when the bulk of the story starts. We first start off in the year 2050 on board the Ulysses, the first starship sent to Mars. Wilson Kime is aboard the Eagle II, the landing craft heading down to the surface. The human race has finally made it to the stars, or at least to the planet in which we've had a fascination with for god knows how long. Not everything works out as it should though. After a successful landing, everything appears to be going fine and on schedule until Nigel Sheldon shows up through his (and Ozzie Isaac's) wormhole in what looks like an adapted 1950's deep sea diving suit, complete with tubes running back through the wormhole to Earth. Wilson isn't best pleased, but now the human race really can make it to the stars...
Fast forward to 2380 and the human race is fulfilling its potential. We have colonized over 600 planets covering around 400 light years, all interlinked by wormholes - the intersolar commonwealth is blossoming. With rejuvenation a part of life, people live for hundreds of years, at least those with the money to pay for the treatment do, but many people take out a rejuvenation pension to help them later in life. Physical death has also almost been completely wiped out. People now back up their memories in storage crystals embedded in the individual which is in turn stored in secure stores in case of any fatal accidents. If a fatal accident does happen a clone body can be grown and old memories inserted into it giving immortality to almost anyone that can afford it.
Dudley Bose, an astronomer for Gralmond University, is studying the 'Dyson Pair' - two stars nearly a thousand light years from Earth that are encapsulated in some sort of barrier. He hopes to record the slow envelopment of the stars - he doesn't expect them to vanish in a blink of an eye. With news of the envelopment released, the curious nature of the human race pushes us towards building the first ever faster-than-light starship and go to investigate.
The story follows the discovery of the barrier, the construction (and attempted terrorist destruction) of the Second Chance starship, the arrival at the barrier and then the observations of the aliens found when the barrier disappears. The climax of this book is the battle that ensues with the Dyson aliens that use the wormhole technology for destructive and aggressive reasons.
Other strands of the story focus on some of the minor characters in this book which are all joined nice and neatly in either the later stages of this book or in the early stages of Judas Unchained. The main sub-story follows the Guardians of Selfhood who believe in an enigmatic alien they call the Starflyer. They believe the Starflyer to be manipulating the human race and that it is behind the mission to the Dyson Pair. Another of the sub-plots is that of Ozzie on his journey to find the adult Silfen, believing that they will be able to answer many questions about the barrier. His journey through the paths is followed, although this thread is featured more in Judas Unchained.
Judas Unchained begins by describing what small human resistance exists on the decimated Commonwealth worlds which were attacked during the first phase of the Prime invasion. Human resistance forces mainly use two ways to fight back: using the Prime weapons (primarily directed-energy weapons) against the invaders, and also disrupting communication between the slave caste and the commanding caste of the Primes.
Meanwhile, the humans in the remaining Commonwealth pursue several parallel plans: (1) developing a set of weapons and warships to defend against the next Prime invasion and/or force the conflict back into Prime space, (2) developing a quantumbuster superweapon based on technology supplied, unbeknownst to most humans, by the Starflyer, and (3) making plans to escape known space altogether if necessary through the use of Colony Ships
The SI is revealed to be somewhat duplicitous, not committing to help humanity, and yet not refusing to either.
Humans decide that there can be no other solution to the conflict than to commit genocide, destroying the Prime aliens entirely. However, it is revealed that the Primes are planning a much larger invasion, which humanity will be all but powerless to stop.
Humanity begins building much faster, and better armed, ships. These ships are armed with quantumbuster weapons, which function by converting the 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 supernova. One such weapon is eventually deployed on the Dyson Alpha forcefield generator, destroying the Prime flare bomb that was interfering with the generator's systems. This allows the mechanism to reactivate, re-trapping the Prime aliens.
Meanwhile, while some humans battle the Prime aliens, others engage in a desperate chase to prevent the Starflyer (in reality, a rogue Prime alien) from escaping the Commonwealth. After defeating the Starflyer's army and encircling the Marie Celeste, a coalition of Commonwealth forces destroy the Starflyer with a massive directed hurricane, freeing humanity from its thrall.