Players and clans can use Chaos points to join anti-factions, opening up a secondary game play aspect. For instance, according to the lore there is a faction of Mahrims that wish to over throw the current leaders of the Mahrim race. 

Joining these factions would open up a new questing chain and new RvR aspects. Joining these factions prevents you from ever going blue until you leave the faction (very hard), but allows you to buy additional chaos rewards that are as good as the RvR rewards, while some can only be obtained by being in a Chaos faction. For instance, new craftable items with the same stats or nearly the same stats as current cratable items, like black knight armor, would only be available to people belonging to a Chaos Faction.