Heh, this reminds me of a game I played where a pirate based amassed something like 2000 ships (screenshots below).  I dunno how it happened and unfortunately I was testing out the "small fleet" setting so I could not mass enough frigates/cruisers to stand a prayer against that many pirate ships.  Luckily I was playing as the Advent Loyalist and had a level 9 or 10 titan.  I attacked the pirate base from one direction with the largest fleet of frigates/cruisers I could muster and sent my titan in from a different direction using another phase lane.  I used its planet capture ability on the pirate base then almost rolled when I saw the pirates bomb their own base for me.  This kept them from attacking me with something like 200 ships each time and I just left the base alone after that.  It was a nightmare.  Especially when the pirates turned towards my titan.  Almost lost the stupid thing too before I could phase out. 

That can happen if the pirates cannot get to their target when the raid is launched, or if they destroy everything on the planet they raid, they'll head back to base. None of those ships are ever going to attack you though.

If you were advent you could use bombers with combination of repulse...... Keep your coronata in and once you had lv 6 it would do short thing of them . Bring in some progens with malice it should kill them even faster...

if your comp staggering my strategy would be imposible because you cannot micro.....

Back in diplomacy 1.00 pirates were very very strong. I had similar problem 1000+ ships in pirate base grav well all with capital ship stats HP 3500+ armour 35+ and dmg 40+. I played vasari and just for fun I wanted to see how many kosutras would take to kill them (kosutras were still doing dmg to ships). I build 20 of them and if I remember correctly it took 50 shots to get rid of them.

Dude if you had 10 level 10 Marza class Dreadnaughts and still didn't win you must be an incredible noob since 10 Missile Barrages will wipe out everything in a moderate area...

Sorry to say, but really you should have won that battle no matter how many pirates were present at their base.

Missile barrage is channelling...you can't give a marza a move order while it's using the ability, otherwise it'll stop using missile barrage...that'd be my guess anyway why nothing happened....

With those numbers I would level up a VL titan and then send it along with a few capital ships with orders to hold position, one all those ships were focusing on the titan I would activate the maw and BAM most of that fleet is now eaten. The Vasari rebel titan can also deal well with large numbers.