The cross-breeding programme results in the creation of the first organic/ timeship hybrid, which the ruling Houses designate a 102-Form. The ship, on the other hand, likes to call herself Compassion.
Certain elements among the Houses attempt to return this timeship to the Homeworld for study, and for force-breeding with other timeships, but the ship is unwilling to allow this. Compassion and her pilot briefly go on the run from their own world's forces. The War King, always more willing than most to negotiate with non-House agencies, ultimately brokers a deal with the 102-Form: but before any breeding programme can begin, events on Dronid reach crisis point.
So far, Dronid has witnessed a kind of deadlock. The agents of the still-unnamed enemy have been vying for power with the agents of the Homeworld, one side using selected members of the lesser species, the other using the surviving members of Faction Paradox. Neither side has pushed the point, and neither side has risked a full-on confrontation. But now the enemy - perhaps having sounded out the opposition - makes its move, and in one brutal operation takes the entire world, threatening to turn it into a bridgehead for an assault on the rest of the Spiral Politic. Forces directed by the War King immediately move in to stop the enemy before it expands its influence any further. No longer attempting to control Dronid by proxy, the Houses' representatives come out into the open to personally oversee the attack.
The War has begun.
For millions of years, the ruling Houses have dealt with perceived threats to history by cleanly removing individuals, or even whole environments, by remote control from the comfort of the Homeworld. Now, however, they're up against an enemy which can counter such moves in kind: and the Houses realise that for the first time in living memory a battle will have to be fought physically. Dronid is only the first of a million sites which will have to be secured by House forces, city by city and world by world. The battle fought on Dronid is therefore the most visceral conflict known since the war with the Yssgaroth. Not surprisingly, it later acquires a mythical status, the Great Houses being both repelled and fascinated by this newly-discovered iconography of warfare. Folklore has it that the very last surviving member of the Grandfather's old House dies on Dronid during this first battle, his body buried beneath the ruins of the capital, the first true casualty of the War. What's certain is that the world is devastated, its surface pock-marked with areas of unstable time (a side-effect of the weaponry being employed by both sides). The locals will soon discover that even the atmosphere on Dronid can make you old.
Ultimately, the battle is a stalemate. Both sides take heavy casualties, and once Dronid's two major powerbases are crippled the world immediately loses its tactical importance. But the enemy's forces are making similar takeover bids on a thousand other worlds, its armies finally emerging from the unseen regions of the Spiral Politic and challenging the Homeworld's dominion over causality. More importance than ever is put on the timeship breeding programme, as the ruling Houses dispatch their (still-limited) forces across the face of history.
Then the Homeworld itself is attacked. The enemy has no illusions that it'll be able to destroy the Great Houses completely, but a large chunk of the War King's arsenal is eradicated in the assault. For many on the Homeworld, the War has until now been a purely abstract idea, a crisis which only affects the outside universe. For them, this is where the conflict really begins.
Back on Dronid, a few members of the once-powerful criminal syndicates survive and begin to rebuild the civilisation. Many Faction Paradox agents come through the conflict alive: though their (House-controlled) leader is no longer present, he has at least enabled them to see out the start of the War, and as a result the Faction's forces are more numerous than those of any other gang.
The War quickly expands across the Spiral Politic, and two rival forms of history clash across the battle-lines of cause and effect. The early engagements are messy and badly-prepared, marked by rushed attacks on both sides. This is the era of the Thousand-Year Battles, although the Thousand Years in question are purely subjective. Many worlds in the middle of the war-zone (which is to say, in the contested areas of causality) become irreparably scarred.
Outside the theatre of War, the Celestis once again attempt to interfere in affairs even though they see the conflict as little more than a diversion. The Celestis are divided as to whether they should support the Houses or the enemy: now they have no real stake in the conflict, it seems to be a question of which side provides the most distraction. In the years to come conceptual weaponry (based on the Celestis' own memetic technology) will be leaked to the enemy by certain elements among the Celestis, while others will supply intelligence to the Homeworld, though the majority of the Houses regard them as both traitors and aberrations.
Though the details remain unclear, the 103-Form breeding programme begins on the Homeworld. This is presumably done with the assistance of Compassion, but as Compassion isn't known to have a great interest in either side of the War it's not known what she's given in return for her facilities. The first 103-Form timeships will soon come into service, timeships which can think, act and potentially even reproduce as if they were part of the organic universe.
Feeling that the Great Houses will now be too busy to notice its operations, Faction Paradox steps up its programme of cultural infiltration from its seat in the Eleven-Day Empire, once again establishing links with various hominid cultures around history. Among those worlds affected is Ordifica, a twenty-sixth century human colony, where the local media has come more or less under the control of the Faction's representative Mother Mathara (one of the Faction's less pleasant agents, by anyone's standards). The War disrupts many Faction lines of communication, however. By this point the Faction's Mission on Dronid has rebuilt itself in the wreckage, but it receives barely any help from the Eleven-Day Empire.
Though Ordifica is the cornerstone of the project, the earliest of the Faction's human shock troops - later known as the Remote - are tested against a House stronghold on Simia-KK98, a world whose history was hotly disputed by the two major sides in the early stages of the War. The attack is a miserable failure, and although in theory the Remote are supposed to be unknown, unpredictable assassins, the Houses soon deduce that Faction Paradox is behind the assault.
In the wake of Simia-KK98 the Faction elects to give future Remote troops a greater degree of autonomy. The Faction's elders are happy to admit that as the bastard offspring of the Homeworld, they're not exactly well-equipped to train the human psyche. Various experimental Remote projects are begun in order to test the limits of the troops, the earliest (in local time, at least) being initiated in North America during the nineteenth century.
The Second Wave of the House Military is unleashed on the Spiral Politic, the first generation of soldiers born from the military breeding-engines of the War King and specifically raised for warfare. The breeding of armies is a complex matter, however, and the approach of the Second Wave is somewhat more fanatical than the ruling Houses might like. The new troop class insists that all offences against the protocols of the Homeworld need to be met with extreme force, and as the true enemy's forces are often too well-entrenched to be worth attacking, the Second Wave spends much of its time seeking out the powerbases of errant groups like Faction Paradox.
The formative Remote colonies suffer more than most. Ordifica is entirely eradicated. Faction Paradox removes its agents there shortly before the calamity, and begins to set up independent communities for them around the Spiral Politic. From now on, the Remote will be on permanent stand-by throughout the War. Should the two sides sufficiently weaken each other, they'll be called into action and pick the wreckage clean.
At least in theory. The question is, with the House Military breathing down its neck will Faction Paradox be able to survive long enough to see its plans come to fruition?
Possibly the lowest point in the Faction's history so far, as its lines of communication are shattered and its resources in the outside universe are destroyed by the genocidal crusades of the Second Wave. There's unprecedented dissent in the Faction's ranks - and this from an organisation for which dissent is supposedly a way of life - which leads to a series of defections, not to mention the founding of a short-lived breakaway sect. Six years later, Faction Paradox suffers yet another indignity when the Eleven-Day Empire is breached by a hostile force originating among the lesser species.
Although this assault causes a fair degree of destruction within the Empire, at least the re-building period gives the Faction's upper ranks a chance to take stock and re-consider their strategy. (A detailed history of much of this period can be found in The Book of the War.)
By this point the War is entering its entrenchment phase, far from the badly-thought-out strikes and counter-strikes of the Thousand-Year Battles. On the Homeworld, military breeding has been somewhat refined, and House society's increasing interest in the purely biological has led to the newly-created Fourth Wave adopting a policy of “bio-diversity”: it's suggested that some of the Fourth Wave cohorts are designed to be able to reproduce without the need for breeding-engines, or possibly even cross-breed with agents of the lesser species.
All of this is approved by the War King, but for the more traditional ruling Houses there's a sense that it's possible to take the concept of alliance a little too far.
A cautious Faction Paradox is still monitoring the few surviving Remote communities, and in some cases even begins to step up the training of its shock troops, though in light of previous failures the Mothers and Fathers who oversee such projects are careful not to push things too far. The Eleven-Day Empire eventually concludes that as it'll be generations before the Remote are suitable for their intended purpose, it might be wise to cut all ties to them for the time being.
However, it's noticeable that the Remote are now beginning to spread of their own accord. Apart from the frequent Remote migrations through the later human colonies, on Earth the (cultural) descendants of the nineteenth century Remote have formed a society of their own in North America. The North Los Angeles Cabal has a significant impact on human culture throughout the 1900s, although its operations are eventually shut down by the Great Houses.
By now, all contact between the Faction and the Remote has effectively been severed. The Faction has become a far more subtle and studious organisation by this point, committed to careful bio-research rather than the grand and sweeping gestures of its past.
It's a symptom of the War in general. The entrenchment phase is well and truly under way, and throughout its history Faction Paradox has always tended to mirror the ruling Houses.
Little Sister Justine is a new initiate into Faction Paradox, and in order to broaden her horizons (her upbringing was on nineteenth century Earth, her recruitment a side-effect of one of the Remote experiments) she's sent to serve her apprenticeship at the Faction Mission on Dronid. Almost fifty years after the start of the War, the Mission continues to vie for power on a world now forgotten by the chief Warring sides. In charge of the Mission at this time is Cousin Sanjira, and Little Sister Justine becomes one of the younger family members under his guidance.
At this point the Eleven-Day Empire controls six large-scale warships of its own, not counting those vessels stolen by the Remote. It's not a huge number, but then, military conquest isn't really on the agenda. Nonetheless, each of the massive, skeletal vessels is capable of destroying complete ecosystems without much difficulty, and the warships begin a campaign of eradicating all those worlds where Faction Paradox has been careless in the past in order to throw the ruling Houses off the organisation's scent. (The worlds erased in this fashion tend to be colony planets where the Faction did once have a presence, but where civilisation has now fallen. Thus, casualties are numbered in thousands rather than billions… at least at this point.)
A relic is uncovered on Dronid, the corpse of a member of one of the Houses, supposedly a great hero who gave his life in the first battle of the War. Giving the dead their due, Cousin Sanjira performs the rite to dispatch the body into the nexus of causality, not realising that the dead individual was in fact the last member of the Grandfather's birth-House: not just a bloodline-relative of the founder, but an individual whose biodata holds certain key secrets which could prove invaluable to those parties involved in the War. (Of course, this makes very little sense. The relic is obviously of value, and yet nobody seems to have ever searched Dronid for it before… or if they did, they found nothing and concluded that the body had been lost. This leads to the suggestion that somebody may have planted the relic in the ruins of Dronid, some time after the battle there, but all this is speculation.)
The relic is lost to time, and on discovering its importance Cousin Sanjira's guilt compels him to offer himself up to Paradox as a punishment. Following his departure, Justine shows potential and is brought to the Eleven-Day Empire to conclude her apprenticeship in the presence of the Mothers and Fathers. She's seventeen years old, but appears older thanks to conditions on Dronid.
As she reaches her eighteenth birthday, Little Sister Justine is made a Cousin, and as a prelude to the initiation is sent on her first mission outside the Eleven-Day Empire. She's dispatched to late twenty-first century Earth, where she's charged with the task of retrieving the relic lost by Sanjira (which has arrived on Earth as a result of the funeral rites).
During the mission, Justine encounters an agent from the Great Houses who originates from a time in her relative future, several hundred years into the War. The Faction is pleased to discover that the power of the Great Houses has been all but destroyed by this point, and that the original Homeworld has been lost. Furthermore, the agent's knowledge of Faction Paradox demonstrates that the organisation must survive for at least a few centuries more. Justine ultimately fails in her mission, but this failure has been anticipated by the Faction's elders: the initiation is, by anyone's standards, a difficult one. Judging Justine to have done well in the field, her elders allow her to undergo the ritual in which her personal weapon is bound to her. Justine's closest confidant in the Eleven-Day Empire is Cousin Eliza, whose origins remain foggy but who was definitely born on Earth. Justine and Eliza undergo the bonding ritual on the same day, both of them nominating the sword as their weapon of choice.
Meanwhile, the relic from Dronid is believed destroyed, its secrets lost forever.
Mother Mathara captains one of the six Faction warships to a degenerate colony world called Dust, on a mission to introduce one of Godfather Morlock's biodata viruses to a formative new ecosystem there. The project backfires, but Mathara discovers certain interesting things in the process.
Though it fails to infect the ecosystem, the biodata virus does find a target on Dust, sinking its claws into an agent of the Homeworld who happens to be present there. However, Mathara soon realises that the timelines have once again become tangled. The agent in question hails from the past, from an era several centuries prior to the beginning of the War, an era before the Grandfather's rebellion and imprisonment. In other words, despite all the built-in protocols of time-travel some of the Faction's biodata has become embedded in the past of the Great Houses.
Mathara concludes that in time, the biodata will take root in its victim: as a result, all of history could be re-modelled. She reports this to the Eleven-Day Empire, which decides to keep a close eye on the past. The Faction's agents now have a kind of Trojan Horse in the history of the Homeworld… they just have to work out how best to use it.
Following the era described in The Book of the War, the events of The Faction Paradox Protocols begin. Cousin Justine is twenty-one years old and serving in the Eleven-Day Empire under (among others) Godfather Morlock.