Battle of the New Day
Shortly after the end of the Alliance era and the Age of the Dragon, the Gudersnipe Foundation began to hide or otherwise destroy most of its millitary assets. It was very clear that given the gap in both numbers and technology, the forces of the Crimson Blade had little hope in preventing the Long Night.
Many ships were given to the resistance then led by Emily Jusenkyou. The Foundation had to appear, at least outwardly, to capitulate in order to maintain at least some small measure of autonomy. Samuel Fate preferred the existing G.A.T.E. network over his previous methods of inter-dimensional travel. Since the GATE network required the lion's share of the Foundation's resources to maintain, this gave them a strong bargaining position while the Alliance crumbled.
The Crimson Blade initial tried to hide its more advanced capitol ships, laying down dragon's teeth for Hunter Jusenkyou's eventual return. However, it quickly became clear that the Long Night was going to last for hundreds, possibly thousands of years, at which point any vessels built during the Alliance era would be useless. Instead, the Foundation turned its attention not towards arming, but towards laying the necessary groundwork to re-arm once the threat had been eliminated.
The Gudersnipe School Proper was kept concealed from Samuel Fate. Given that it is also the likely meeting place for the Blind Counsel, this allowed the Foundation to continue covert weapons and technology research. Most of the top scientists and all of the research from the Victory Research Facility were transferred there, with Joshua Jusenkyou placed in charge of weapons development.
Being largely cut off from the rest of the verse, the school lacked the resources to build any significant military assets. However, with new technology developed by Joshua, they could at least match Fate's forces technologically.
New Day Fleet
By the end of the Long Night, between new ships built specifically for the battle, refit ships kept mothballed over the period, and other ships hastily salvaged and made battle-ready, Joshua was able to assemble a fleet of around 1,000 ships. Along with this were over 200 highly advanced mecha built by the VRF that had been maintained (their pilots kept in stasis).