Roots:

• Ephemeral
  • Fleeting, lasting for only a brief time
  • ...or in our case, only percieved/present briefly, fitting for a ghostly espionage-based faction
• Myriad
  • Of countless or extremely great numbers
  • These beings are countless in many ways, nobody can truly guess or would even be able to observe them long enough to count their forms, their numbers, their lifetime... 

You could also possibly associate them with ephemeris, the word for a journal that tracks the positions of astronomical objects, relating to their seemingly cosmic origin and tracking of other astronomical objects (read: empires).

How I chose the name:

We don't know too much about this race of cosmic wraiths (likely neither do the rest of the factions), so I wanted to go with something mysterious and alien, while also sounding official enough for a faction to use to describe such a race. I also wanted to capture a bit of the beauty of an ancient race of cosmic wraiths- both ephemeral and myriad have poetic connotations.

My vision of the race:

One of the reasons I went with "myriad" is because I imagined these beings as a sort of collective (in such a case I would call them "The Ephemyriad," if it turns out that they are more individual then instead I would call them "The Ephemyriads"). I tried to create such a believable english-based name is because in my mind, The Ephemyriad would not have seen any meaning in naming themselves until they came into contact with other empires who took it upon themselves to do so.

I don't see them as good or evil, and they aren't particularly vengeful like the Harmony or desperate like the Riftborn- rather, they seek to end their isolation, obscurity, and ignorance of the galaxy and replace it with presence, awareness, and influence. They desire ultimate control- not for the power or the ability to protect the galaxy from itself, but because they view it as the most logical way to preserve their self-determination after having witnessed the chaos of the Endless and recognizing it in this new galactical strife.

EDIT:

Thanks to a suggestion from Aitarus, I am also considering "The Ephemeral Myriad" for their faction, with Myriad being their government type, and Ephemeris being a simpler and more genuine-sounding name for their race.

I would actually be on board with just 'Ephemeris' - the etymology for this is very nice - and have 'Myriad' be their government type, like all the current factions have their in-lore organisation i.e. Vodyani Protectorate, Aurigan Federacy - for these it would be the Ephemeral Myriad.

The blend word feels a bit too manufactured to be a natural name.