and the crazy thing is, it seems as though Agony Empire never forked over the 3bill. There's so much metagaming, politics, and mind games going on over this it will take a very long time to sort out the future ramifications for both alliances.
Since most don't play, much less follow EVE goings on I'll try to sort it out a bit. Hydra has a reputation as a 'Troll' alliance. They do sneaky, devious, trollish, underhanded/whatever both in-game and on the forums just for the grins and giggles. You trust them about as far as your guns can shoot them. Normally in piracy what will happen is someone gets their ship incapacitated, and the pirates will ransom the ship (you give them X isk in return for not destroying your ship), and if you pay up they let you go. Hydra Corporations (and a few others) are known for getting the ransom then just blowing up the ship anyway.
Agony Empire on the other hand, is a decently well known but small PvP Corporation generally known for helping newcomers into the PvP experience. Like most smaller alliances (the one I'm in included), they choose to remain out of the forums to avoid attracting the unwanted attention of more powerful and generally chaotic entities (like Hydra).
Now that we have a general idea about both allliances, we go to the Tournament itself. Hydra is there for the lulz, they don't care about winning or losing, they are there for the splash they can make (and considering their skill, not something that can be easily brushed aside). Rumor has it Hydra had planned to blow up their ships and throw the fight regardless of getting paid. There are a few very devious reasons for doing this:
A) It adds to their reputation in the most public, high profile way possible.
B) It sets them up with a much, much better chance at winning their next fight.
C) It seriously undermines the morale of Agony in their next match. They (and everyone else following) know that they are not supposed to fight the next opponent, and what is normally going to be an underdog match is going to be made much harder by this.
Agony is there for the honors. Despite the Tournament setups being vastly different from what is normally used, the pilots skills and the leader's knowledge on what to do in any given situation is still the same. A win or two is all that is really necessary to show they've got teeth and are more than capable of giving people a run for their money -the goal of all PvP corporations.
Now in terms of the affect on the game, politics will get hairy -especially for Agony. Those guys lost in more ways than one. Hydra claims Agony paid up, Agony says they didn't, no third party was used to confirm either way. That's an ugly mess right there. General consensus is that Agony didn't pay up, but still the otherwise stellar reputation is tarnished (and in EVE like the real world, reputation is everything). Second, they put themselves squarely on the map with the potential to become a liability to nearby and currently friendly alliances if other PvP corps decide to stop by with the intention of spreading a little destruction considering how easily the team went down that match. Though if they win their next match, they'll not only regain any lost honor but they won't even need to win the Tournament in order to consider themselves ahead. If they lose... They'll be looked down with pity at best, a very bad thing for a PvP alliance.
And that's EVE. All or nothing, utterly cold and heartless, incredibly complex. Just like space itself...