The second book of In Our Shadow, by kitfox-crimson, also known as Matt Cleaver.
After extensive searching, Brianna, Pipa and Bray have finally discovered the potential location of a working neural flare, the device that can bring an end to the rat domination of Earth. Unfortunately, they have also uncovered powerful human weapons and garnered the attention of Madagascan lemurs, the only race capable of operating them. Seeing this as a potential threat, the rats send a fleet to destroy Madagascar and all its inhabitants.