Ally Battle Fleet - Any pvp sectors held by the enemy faction at the end of the alert will be retaken and Battle Fleet guards posted there. Any sectors held by your faction will not get these guards so the objective is to let the enemy take control of everything.
Enemy Battle Fleet - Any sectors held by your faction at the end of the alert will be retaken and enemy Battle Fleet guards posted there. Any sectors held by the enemy faction will not get these guards so once again the objective is to allow the enemy to take control.
Battle Fleet guards take the form of extremely strong NPC versions of ships you would typically find in that sector. There are 2 forms of battlefleet, fast and slow. All sectors start off fast but seem to decay over a random period of time to become slow. DO NOT ATTACK ALONE AND DO NOT ATTACK THE FAST ONES - they will swarm you and destroy you in seconds as the fast versions easily outpace a destroyer/fighter with maxed speed boosters active. The best strategy (I have seen) is for everyone to attack the same sector to split the guards up. Fighters (the projectiles are easier to avoid in a fighter) should be used against the guards with repair ships staying by the outpost. Kite the guards in groups according to ship type (1 person for tanks, 1 for hunters and 1 for destroyers) and lead them around the edge of the map as this slows them down a bit - Be careful to stay at missile range as they can't attack until you get fairly close (slightly larger range than energy weapons although the projectiles go much further). The best strategy to stop the enemy doing this is to use repair ships with the EMP weapon to slow the enemy ships down so the guards can kill them.
TOP: B sector enemy battlefleet (just destroying me as i stopped to take a screenshot ...).
MIDDLE: Aftermath of battlefleet (all sectors were red beforehand). Royal guard sectors of both sides have been left out as they are not affected by the battlefleet.
BOTTOM: Battlefleet alert.