Rainbow factory was the first fan music I’ve ever heard in the brony fandom, and it is definitely one of my favourite fanfics.  
In my own fanfiction rainbow factory 4 (which is in Chinese), the rainbow is used as the ammunition for the elements of harmony, which is in turn the equestrian equivelent of nuke. Once the rainbow factory is destroyed, the equestria no longer hold the strategic deterrent, and the combined force of zebra and dragon invaded immediately before Equestria could rally an army. This is also the reason behind the ability setting for Rainbow Dash in the legends of the three kingdoms project. She can protect allies from damage, but every time she does so she risks dying.
 
再酷廿分 云宝黛西 9999  
设备 每当有角色受到伤害时，你可以把一张牌从手牌中置于你的武将牌上，称为“虹”，然后防止该伤害；每当你受到伤害时，伤害来源可以把一张手牌作为“虹”置于你的武将牌上  
迷失 锁定技 当你的武将牌上有七张“虹”时，你须将它们弃置，失去“设备”，并把体力值调整为1