Vivarium
The Empire has a thorn in its side. That thorn is the Vivarium.
No-one knows how they began. No-one knows how they will end. Almost all of the Vivarium is shrouded in mystery. It is often treated as an opposite number to the Empire, even having its own immortal leader: the Regnum.
The Vivarium is separated int 6 Kingdoms, each named after and based on one of the Kingdoms of life in the First Earth accounting of species: Protista, Fungi, Archaea, Bacteria, Animalia, and Plantae. Each are deeply dedicated to their role, often biomodifying to have some of the attributes of their designated Kingdom.
Recently, Animalia is known to have murdered Archaea. A trial (of a sort) is currently being held on Old Earth to determine who chooses Animalia's punishment--and yes, Animalia is one of the competitors. Protista, while required to compete, is not trying very hard.
Public Agenda
To free Meliora from the tyranny of the Empire; to free Synthies and make them equal to born humans; to destroy the Empire.
Enemies
The Vivarium is a huge thorn in the Empire's side. That being said, the Emperor himself seems to find the Vivarium more of a nuisance than anything else.