Both the Jedi and the Republic hierarchy knew full well that the truce between the Jedi factions could not survive. Tensions soon erupted between those bickering rivalries, unable to resign themselves to consensus or give up the principles for which they had been fighting for years. Furthermore, as Jedi were killed in battle, the rise in vendettas against those who had struck down comrades grew, and an endless cycle of vengeance and reparation began.
The corporations who had supported the various factions likewise remained unconvinced that another tectonic shift in the galactic economy was not about to wreak havoc once more. Not only that, but they had begun to profit in a fashion from the conflict itself, a situation that few of the big corporations wanted to see an end to. Rather than a middling peace treaty, the econocrats of the Republic demanded a full-scale treaty, a signed and legally enforceable guarantee of galactic security. Anything else, they believed, paid nothing more than lip-service to the well-being of the Republic and its citizenry.
While the Council of Hapax had initially been seen as a great success, negotiations inevitably broke down, and in little more than a year the Jedi returned to their doctrinal conflict.
Senator Palpatine, a leading voice among the opponents of the Jedi Order and its disruption, leapt at the opportunity presented by the renewal of the war. He authored and successfully lobbied a series of legislation which punished internal disorder by suppressing or outright removing the extensive privileges enjoyed for centuries by the Jedi Order. Most notably, Republic governors were granted extensive powers, and became the new arbiters of galactic law. As the Jedi before them, each dictated the obedience of a single planet.
Eventually, the Jedi Council itself was expelled from their own grand temple on Coruscant, and scattered to distant locations throughout the Core Worlds. The temple was, for a time, retained as a relic of the old era and intended as a future museum to the mysterious Force of Others and its adherents.
The Republic Senate concurrently established a new, enhanced and much more potent, military force, one raised to defend the people of the Republic from any internal or external threat - few were so blind as to not recognise that this threat was now, inferred or otherwise, the Jedi.
Little more than a year after the Council of Hapax, the Jedi fell back to war, and this time the entire Republic along with them. The war-weary public sought an end to the violence via their representatives in the Senate, yet the Jedi to their detriment would not heed them. For a second decade, the Jedi waged terrible battles across the many sectors of the galaxy, further damaging their reputation and their numbers.
Yet they now faced a new complication in the form of an organised and substantial Republic military, which often stood directly between them on the field, or restricting access to an ever-growing list of protected Core Worlds, forcing the conflict into the Outer Rim, or the harsher and less hospitable planets of the Core. Casualties increased, and the cost of the war, in manpower, materials and credits, began to swell.
And the Jedi themselves were no longer at the head of every army, but reduced to commanding several armies or fleets at once, though intermediaries and subsidiaries. Always seen as aloof and distant, the Jedi had now become so even to the forces fighting in their name. Many armies had become entirely composed of mercenaries or even criminals; anyone who would take up arms on behalf of the once-revered Order.
At last, even the vaunted Jedi recognised the inevitability of their approaching fate. To their horror, they discovered that with their numbers so dwindled, the Order had lost substantive control over the judicial system the once oversaw and, even more significantly, recognised how far they had fallen in the hearts and minds of the common citizens of the Republic; the people they were sworn to protect.
The Jedi had always held a complicated relationship with the political and ruling classes of the Republic. The old nobility and especially the Galactic Senate frequently viewed the Jedi as elitist and unaccountable for the incredible power they wielded. Control over such a broad range of judicial powers gave them unprecedented moral and temporal authority in the galaxy. Particularly whenever their sphere of authority conflicted with the interests of the other branches of the government, or powerful corporate or private interests, this created a great deal of resentment and resistance.
Yet there was little the executives and Senators of the Republic could do while the Jedi remained so popular with the people. Radical legislative change had been defeated time and time again precisely because, for better or worse, the Jedi had in fact maintained order on almost every planet they oversaw. Every opportunity to stifle their power was overruled either by the Order itself or enough Senators to oppose such a bill, and frequently shouted down by popular acclaim. So the loss of such support was a critical blow to the Jedi and their cause.
Thus, when the ruling classes of the Republic sensed that the Jedi were vulnerable, many began to relinquish their support for the Jedi factions themselves, and began to agitate for wider reform which might forever limit the influence of the Jedi over galactic affairs. The passing of Statute 12-22j-5a4, a meaningless stream of figures to the average citizen, was crucial in this endeavour, for it mandated the need to replace Jedi authority in the courts with elected officials, in the case of the Order's fracture. It was Palpatine's crowning achievement and saw the Senator become a symbol of definitive action in a time of uncertainty.
Thanks to the ongoing war, the statute not only passed but went into immediate effect, ending the Jedi stranglehold on the judiciary and relegating them to political exile from within their protected enclave among the Old Republic's vast bureaucracy. Not only had they lost their temple - a symbol of their power and prestige at the centre of the Republic's seat of power on Coruscant - but they had also lost the legal authority to act as they had since the early days of the Republic itself.
Let it not be said that the entirety of the Jedi Order remained ignorant of their fall from grace, or that there were not impressive voices within the remnant who had not called for an end to what they viewed as the inherent insanity of war. Many took the opportunity to hearken back to older times, during eras millennia past, quoting esteemed masters such as the classical stoic, Yoda, and the doctrinaire Ulic Quel-Droma, who had formulated and written the Jedi Code itself.
Many Jedi departed the Order during both conflicts, fleeing to the Outer Rim, or allying themselves with forces ready to restore something akin to a system of rational and natural justice. Most of these self-imposed exiles had become disgusted with the hypocrisy of the Order's stance, and its inability to apply their own traditions to the petty feuds which had torn it apart. Many were even resigned to a greatly diminished influence; anything that might sate the furious peoples of the Republic and restore peace to the galaxy once more.
Over the course of several months the Jedi Council, despite remaining fractured on many issues, managed almost miraculously to reach a consensus on the path forward.
With the growing power of the Senate and the sheer weight of resources brought to bear by the corporate supporters of the Republic, the Jedi had little choice but to overcome their differences and reunite, in order to reclaim their control of the judiciary and reassert their form of justice throughout the Republic. Though many felt it was too late, the Council in particular was of the view that the galaxy still needed the Jedi Order if there was to be lasting peace.
At the Council of Bakura, in a more desperate mirror to that of Hapax, the three most prominent Jedi factions reunited in order to face the combined threat of the Republic forces which had morphed from interceding on behalf of key planets to actively pushing the conflict further into the Outer Rim, and also to heal the schisms which had divided the Order itself. But for the Jedi, it was too little, too late.
The Council acted with haste, and in an act of undeniable irony usurped control over a radical new technology created on the planet Tython by the Spaarti Corporation. This was a step too far for many Jedi, particularly those who had returned to their study of the old ways, in which the Jedi were first and foremost beings of the Force, luminous and beyond the temptations of the physical realm: that of crude matter. The Jedi were, if nothing else, above such things and to turn to them even now was tantamount to ultimate defeat, no matter the mere political outcomes of the war - which were trivial in comparison.
Within this most important few weeks of the Second Clone War, the Jedi had gone from commanding vast resources and directing a plethora of vested interest toward their own war goals, to becoming outcasts from their own Republic, facing down the combined might of the Galactic Senate, the civilian military, and several ruthless corporate interests, only to unite in the face of the very conflict which had seen them ostracised in the first place.
Turning to Tython and its new technology, now known as Series VI, the Jedi began creating clones of their greatest warriors, and set in motion a terrible chain of events which would bring about the end of the war for good.
For all their prescience and meditation, the Jedi had not seen the seeds of their own sown in this fateful decision. Scholars continue to debate how they could have come to such a radical decision through anything other than sheer desperation, for in hindsight it seems a folly of catastrophic proportions.
The return of the Jedi, many of whom were believed to be dead or grievously injured, and the Order's new-found dominance of the battlefronts trailing across whole sectors of space, did not go unnoticed among the leaders of the Republic. The tide was turned, and the Jedi began clawing back control over key territories even in the Core Worlds, all within months of having appeared on the very verge of defeat.
While the Republic leadership had indeed struck a key and unforeseen blow to the Jedi at its moment of greatest vulnerability, it did not take the Order long to recognise that the Republic itself now viewed the Jedi as, at best, an insubordinate or, at worst, a mortal enemy.
After long months of war, the Battle of Corellia resulted in a particularly damaging loss for the forces of the Republic, and resulted in the Jedi moving within striking distance of the capital, Coruscant. The end of the war appeared close, and the Republic generals knew it. They also knew that, without a counter-turn in the tide, the Jedi would be victorious.
So too the Senate, sitting in emergency session on Coruscant, held no qualms about the singular means by which they might resolve such a grave circumstance.