First Contact Uprisings

Revolution

The Alliance's Covert Uprising project results in a large-scale military conflict.

The First Contact Uprisings was a violent conflict that stemmed from the Systems Alliance 's now-defunct "Covert Uplifting" process.
During the early years of the System Alliance, the member states were faced with a difficult dilemma; They had found several sentient races at various stages of societal and technological advancement that was within their territory, but who had not yet mastered space travel. The humanists argued that it was inhumane to let these natives live in societies ravaged by disease, violence, and scarcity when the Systems Alliance possessed technology that could save them. The Conservatives, however, argued that these societies were not ready to join the galactic community and that Systems Alliance intervention would irrecoverably damage their cultures and natural progress.
The compromise was the Covert Uplifting process. It was decided that when a planet was discovered, Systems Alliance officers would covertly infiltrate their society and advance their technology without actually making First Contact. This way, technology, and society could reach a point where they could join the galactic community without forcing it on them, it was reasoned.
How, exactly, it went wrong is unclear (Though conspiracy theories are numerous), but within a single year, every one of the Covertly Uplifted societies became aware of their alien infiltrators. First Contact was made and all but a handful of the planets reacted with horror and rage, rising up against the alien agents in their midst. Stealing technology that allowed them to venture into space and fight back, in many cases integrating it into their own technology (Which had been made more and more compatible by the Covert Uplifting). While there was no real threat to the Systems Alliance as a whole, the rebelling planets was a threat to civilian life in close proximity and Systems Alliance ships were dispatched.
As many Systems Alliance members saw this as entirely the Systems Alliance's own fault and the Uprisers as innocents, the military response was fragmented and many planets opted to, rather than attack the Uprisers, instead fortify their own defenses. The weak response made the war drag out by years, with increasingly bloody conflicts. The Uprising never really ended, but most of the fighting stopped when twelve of the uprisen planets created the Union of the Unaffiliated and signed a peace accord with the Systems Alliance. Many of the others would eventually become Unaffiliated, while a very small number of those who had responded more peacefully to the infiltration ended up joining the Systems Alliance. To this very day, in areas carefully quarantined by Systems Alliance ships, there are a few planets who still consider themselves at war and who occasionally try and attack outwards. Usually, their ships are disabled and sent back without casualties, but their technology advances every time.