The four factions

After the Zao reveal, you learn who holds the Citadel shut. When heroes pinned the Unburied King in his Citadel long ago, three orders of Etzel's line and the naga seers each took a binding seal. Now the Rot is corrupting all four guardians. Each is a self-contained tragedy of a vow kept too long. Together their four Seals form the Sigil of the Unburied King, the key to the Citadel (Seals and the Sigil of the Unburied King).

Faction	Pinnacle	Home	Encounter in your maps
Lion	Drume the usurper	Bounac and the Lion Sanctum	Lion Caches: locked chests behind a keeper (Lion Caches (Drume))
Falcon	Grand Master Oberon	Falcon Bastion and the Secret Library	Falcon Rifts: waves from a tear in the wards (Falcon Rifts (Oberon))
Cobra	Scarlett Etzel	Cobra Bastion and Kilmaresh	Cobra Reliquaries: freeing trapped monsters (Cobra Reliquaries (Scarlett Etzel))
Naga	Timira the Many-Headed	Marapur and the Emerald Gardens	Tide Shrines: shrines that grant Voices (Naga Tide Shrines (Timira))

Order. Do them in any order. None needs another.

Progress for each faction

Open maps with that faction as your Focus (Atlas Focus).
Meet sites and their mini bosses: Captains, then Champions, then the Hold's Warden. Mini bosses get Swift, Armoured, Vengeful, Summoner or Warded modifiers, plus a signature modifier (Monster modifiers).
Earn Standing Points and Tokens (Standing and Tokens).
Clear the faction's Hold to earn a free Writ (Faction Holds).
Defeat the pinnacle to earn the Seal (Pinnacles and Writs).

Mini bosses. Lion: Ancient Lion Knight, Archer, Warlock and the founder Kesar. Falcon: Grand Commander Soeren, Preceptor Lazare, Grand Chaplain Gaunder and Grand Canon Dominus. Cobra: Neferi the Spy, Sister Hetai, High Templar Cobrass and Scale-Warden Ashkara. Naga: the Corrupt Naga Seer, Naga Tideguard, Mountain Voice and Bile-Mother.

Status: the four mechanics and their mini bosses are in the game. Holds and pinnacles are coming soon.

Related: The Atlas, Unique items.