In Star Wars Battlefront II (2005 and 2017), we see Darth Maul in the side of the Separatist. In the Phantom Menace, The Confederacy of Independent Systems or the Separatist is not yet formed only the Trade Federation is seen.However,in the next movie(Attack of the Clones up until Revenge of the Sith),The Trade Federation is now in league with the CIS. During the battle of Naboo, The Dark Lord of the Sith Darth Sidious sent his apprentice, Darth Maul to assist the Neimoidians Viceroy Nute Gunray and Rune Haako. So let's compare the villains in Star Wars with their association in every factions.
- Chancellor Palpatine/Darth Sidious/Emperor Palpatine - (Republic as Chancellor of the Republic,Separatist as Darth Sidious, Empire as Emperor)
- Count Dooku/Darth Tyranus - Republic(secretly) and Separatist
- General Grievous - Separatist
- Jango Fett - Separatist
- Boba Fett - Empire
- Grand Moff Tarkin - Empire
- Darth Vader - Empire
So looking at those individuals, Darth Maul is the only villain that doesn't have a military faction.Which makes me wonder if he's included in the Separatist Movement.Despite he is just assisting the Trade Federation during the Battle of Naboo. Not to mention that every apprentice of Darth Sidious has a military group like for instance: Dooku/Tyranus to the CIS and Vader to the Empire.