Well the problem with that idea is that players wouldnt want 2 loose that shiny 3million cryo parsec and all there 85 levels, perhaps you "wake up" (in the ship you where flying in the final SM) surrounded by these aliens, you may choose weather to attack them or not, then you have a faction in the war between evil humans or good aliens, if you attack the aliens you become evil.
Alien Start:
you soon get hailed by an alien ship, and they ask you to accompany them to their headquarters, then you find all your ships in a hanger, the aliens tell you that your jumpship was sucked into the "hole" in the continuum, with all your ships, however, you also have another ship, it is a ship from the aliens, it looks very different and has no abilities, its first ability is: cannon (this is more like a powerful single shot blaster) its second ability is matter converter (fancy name for collector) its third ability is: Matter Purge (repairs your ship instantly, with longer recharge time than repair droid) and forth ability is: teleporter (this ability instantly teleports you ahead of where your ship is facing) then you will beable to choose whichever abilities you want, however these will be looted from the evil humans, out of existing abilities and a few new ones, Including: Plasma Thrower (this is like a fast charging rocket doing about 35% of the damage a rocket would and has no area of effect takes about 7 seconds for a full cycle) EMP field (all enemies are 25% slower for a certain amount of time) Point Defence Drive (a passive ability on your ship, this is a small turret on your ship which you toggle on and off it will attack enemies and also occasionlly destroy enemy rockets) and I could come up with new ones all day, The alien ships are very large and well armoured (about twice the size of the methanoid battlecruiser thing or vandetta) however are much slower than normal ships)
Human Start:
After you attacked the aliens you almost immediatly get destroyed and the aliens "throw" your escape pod into space, you soon after are picked up by a human cruiser patrolling their base planet, you are then taken to training grounds in order for the humans to have some idea of your skills, they repair your ship and you pass there test with flying colours, they are so impressed with you that they give you a choice out of 7 types of vessels: Storms, Tanks, Shocks, Engineers, Snipers defenders and a special modular class, which the last 4 abilities you may choose, you pick whichever you want and have it kitted out with the sub-standard stuff of pirate galaxy part 2 (see down bottom for further details), then you do a few nice easy missions and you get your ships back, the human ships are alot more like the ships we know on pirate galaxy, however they are not better or worse than the alien ships, they have less armour and are alot faster, also they do more damage, destroying an alien ship is more than possible in human ships.
Both plots: about 1/3 of the way through both plots you come to a point where the sector is invaded by an unkown race, both factions sign a treaty to fight against the invaders, now both factions may accociate with eachother.
You may have heard me say "pirate galaxy part 2" this reffers to the game after sirius, it is like a restart, however you still have all your own ships, cryonite and levels, you may leave pirate galaxy part 2 at anytime and go back to part one by going through the the subspace tear (which looks like someone has "ripped space")however even in part 2 you may talk to fellow players in public and private chat rooms even if they are not in your faction, however you cannot help them until they have gotten to the point where the alliance is made.
Pirate Galaxy Part 2:
-the worst equipment from PG Part II is about 20x better than that of rare sirius bps
-Stuff from part II cannot be taken to part one, your PG part II ship can only be used in part 2 aswell as if you where to put any PG part II equipment on a part I ship for some reason.
apologies on such a long comment, ill probally make it in to a post oneday lol