The idea is simple. Every once in a while, have certain NPC groups lead a mass invasion of a territory. For example, the Separatists might invade Blazeridge Steppes. The invasion force will consists of a few hundred NPCs and will battle across the whole map (similar to WvW, but against NPCs). Assuming they start from the south, the NPCs will slowly fight northward until they over take the whole area, if they can.
The NPCs can get really creative. For example while attacking Splintercrest Fort, they might also attack Soot Road to stop that Asura gate from operating. And with the players trapped inside Splintercrest Fort, they will go attack other areas unhindered.
30 minutes before such event takes place, there will be a notice to all players in the server. That gives the players plenty of time to get to the area to help out.
There are two possible outcomes:
1)If the NPCs were beaten back, then the area carry on as it did.
2)If the NPCs win the invasion, that territory would fall under their territory for the next 12 hours. None of the heart quests can be taken during this time. There would be temporary world changes. For example you might see Separatists keeping Charr prisoners in little cages and threatening to eat them, etc.
These NPCs doesn't necessary have to be red (hostile) to the players. They can be yellow, so the players had a choice to either fight them or just go explore the area. In the Separatists' case, they might be friendly to humans and Norns, yellow to Asura and Sylvari, but hostile to Charrs. If you are human, the Separatists might even chat with you and convince you to join their cause. (You can't actually join them obviously. But they will try to convince you.)
Either way, after 12 hours, the "good guys" will organize an attack to take back the territory. In Blazeridge Steppes, it would be the Charrs who gather a few hundred NPC allies and strike back. The players can join in the fight with the alongside the Charrs. Once the Charrs win, that sector goes back to how it used to be.