I made it! I did read thru all posts here
Well, I do like the suggestions all and I think the story line should be so long that it could have implemented all above mentioned, maybe with some balancing modifications.

Comments for post from Epicownage:
- some players on forum refused to have territory implemented (or anything similar to a map) viewtopic.php?f=6&t=32376
- personally I would give a chance to implement territories so we could fortify them, but it would require a lot of work for Dan just for this part of storyline
- reinforcing should not be an activity done prior the invasion = planet blockages, legion base blockade/infection should starts at some point, so the galaxy would be alerted (just a logical background to this first stage)

NPC attack part - maybe we could have it modified to Silthion NPCs invading our "territories" (planets, bases) including our ships?
More in next post, with review of concept I suggest - mainly from my view, using ideas from sci-fi stories and games.

This post is mix of comments and my suggestion/concept modify the suggested storyline (by mojo) and make it last longer.
Have to mention right now, I did try to focus on grammar but I am not native, so please forgive any big typos and focus on content.
I think, the suggestion from Epicownage posted above would be possible to combine with my suggestion:

I would suggest also the galaxy wide invasion, but please do not call it yet war. The story would have several chapters.
- it would be first higher rate of planetary events of now known NPCs (NPCs entities on run looking for new territories) details bellow.
- the real galaxy wide invasion would be invasion of bugs like NPCs - Silthion (this mission chain is per wiki not ended)
- the Silthion would engage their invasion from distant part of our galaxy (let's keep the idea of attack from another galaxy for a little bit later)
- first mission minimum rank 1000, last mission starting at rank 2200 or higher
- Silthion ability random pick from:
----> Metamorphose - turn the occupied planet into Exotic planet (the planet would gain size +1, resources per Exotic planet)
----> Disguise - increase planet cloak by 5000 or by 10%
----> Consume - Digest the planetary resources, decreasing any production higher than usual for Exotic planet. Planetary effect, each day consume 1 resource availability (drop down by 1)
----> Silthion cocoon - after 14 GL days of occupying the planet, a new Silthion is born and travel to next planet to occupy it (applicable if solar system implemented).
- Planets hold by players on mission in outer galaxy would have the legion bonus of legion in which the player is member, while a player can be member only of one legion regardless of the galaxy.

Chapter I: When all went wrong...
1st mission
- planetary events across galaxy - increased NPC blockade of regular NPCs (they run before the new stronger NPC race)
- goal, identify the reason of this increased activity - at the end find a new Silthion NPC after it invaded your planet and it is occupied by Silthion (planet turned in Exotic). This would beht Silthion Larva
2nd mission:
- revealed the reason of increased NPC activity = it would be the attack of Silthion entities across galaxy
- start of Silthion invasion on planets (regardless if occupied or not) and the goal of mission 2 would be to kill one of these to study it.
3rd mission:
- we would find out, that Silthion act as insect and follow the orders of their Queen. (this mission would require a lot of RP)
4th mission:
- locate the Silthion hive - 5000 scan required, spawned in NPC slot, random spawn chance, have to disable Silthion warriors (act as patrols) and eventually find the hive
5th mission:
- cooperative battle of 10 players to destroy the hive and attempt to kill the Queen. 8 hours time limit for collecting 10 participants - 100 energy spent for each alerted player, attending player must have the 5th mission unlocked or already done. Hive would act as NPC base available in Enemy bases or Legion mission.
6th mission:
- kill the Queen by using new CTlab artifact - "Petrifier" and eventually destroy the Queen (get s trophy and module ship - max 4 of them, adding hull and defense boost)
Mission chain final information: The Queen sent prior her death a subspace call for help.
"Petrifier" - froze the target's sensors and decrease the battle activity by 10%.
Silthion Queen would be here an elite NPC matched per rank of the alerting player. I would suggest the details per already discussed suggestions of new NPCs including those from Epicownage.

Chapter II: Hunt
Mission 1:
- studying 10 trophies (each consumed, each trophy to study would cost 500 energy) we would find out that invading Silthions are as result of genetic manipulation for which was Prejor technology used. Reward - blueprint of the technology to create weapon more effective against Silthions.
Mission 2:
- create the technology (create ship module), analyze it and use to boost your strength against Silthion NPCs
10 times: 100 energy, 100 Prejoran Tech, 1x Silthion Trophy and 1x Dominion cannon Mark III (TBD whether we would have only Queen Trophy or also Warrior Trophy - warriors trophies could be required in higher number)
Result: "Dominion channeler" (size 20, attack 200, bonus 5% against Silthions, max 3 per ship)
Missoin 3
- test these weapon on Silthion Hive and Queen. Could be done as participation in mission 5 of chapter I.
Final information - the technology created based on available information is working. We also confirmed the theory of our scientist, that the Prejor tech was used for modification of Slithion race. The modifications on Silthion race specifics show patterns of technology used by Strylls.

Chapter III "Who is the enemy?!"
Mission A:
- engage spy activities on known Stryll outposts while war with Stryll fraction is declared (disable 300 Stryll ships)
- find 10 Stryll outposts and disable them to obtain new information (similar to Zolazin base mission "Vornexa's Taunt")
Mission B:
Stryll: "Race"... why you attack us?
Race: Don't try to fool us, we know that you are behind the Silthion invasion!
Stryll: We were only studying some very old technology from excavations. Nothing of your business.
Race: It is our business when the collateral damage impact also "race" territory.
Stryll: You had proven your strength, so why are you here?
Race: We want you to stop the Slithions invasion... on return we will stop our attack on your ships and outposts.
Result: Start negotiation of truce...
Mission C:
- negotiation interrupted by attack of super-carrier of unknown origin on both Strylls and "Race"
- evacuate the area (mission, required to use 100x Void Shell)
Mission D:
- tracking of the super-carrier from long distance till it reach a huge wormhole
- attack the ship and test the battle capabilities (require using weapons based on Prejor tech and 100x Crux Amplifier)
- aim to disable the ship which ends with major damage on super-carrier but prior last hit the ship a group of other super-carriers arrive thru the huge artificial wormhole.
Missoin E:
- retreat from battlefield (mission, require 100 Dark pyramids)
- "The outer enemy": Backup forces of new enemy start to attack the legion bases - disabling all weak and not well guarded ones = act as target base lock by other legions (8 hours), if the Super-carrier disable the legion base, base is taken over by NPC and all production is consumed by NPC until the base is not repaired and another attack of the NPC is repelled (base not disabled within 8 hours)
PS: New technology of base cloak would be implemented in the game as next research tier for cloak and unlocked after first repelled super-carrier.

Chapter IV "Where two fight..."
- mission chain, where Crimsons getting on power using the captured technology from abandoned Stryll outposts, using few Silthions cocoons to invade planets
- mission chain under concept, basic ideas is per example of Ba'al (goa'uld) who gain a lot of technology, power and territory by recovering the technology of others too weak to defend them.
- this could be part of new race implemented with ability to take over other race ability (similar idea was already suggested on this forum). change of race ability would require 500 energy, critically successful raid ship of the given race (kidnap a crew member as a new host). Cool down - maybe 20 GL days?!

Chapter V "Revenge is a dish best served cold, ice cold"
- rank 2200+ mission chain:
- it will require to secure the giant wormhole from both side = travel to the outer galaxy from where super-carriers came.
- each player volunteering for this mission would gain a contract with Federation of republics and obtain daily shipment of 50-100K artifacts (planets can not travel between galaxies)
- the contractual shipment could grow per mission progress till a new legion base in outer galaxy is established.
- 1st mission to destroy the guarding 2 super-carriers within 8 hours, each shareable with 10 players. This would allow you to find out, that super-carriers are actually huge NPC cyborgs.
- 2nd mission: Survival travel thru new galaxy, find new allies (players), form a group escaping the cyborgs and eventually in hide place build a new legion base (like Battlestar Galactica)
- 3rd mission would lead to establish a new legion base (collect Prejor tech in new galaxy)
- 4th the control over the giant wormhole is lost - players have to create a new smaller version, cooperation in both galaxies will be needed to reestablish the wormhole. This would require a new huge special size module on lvl 7+ legion bases. If the module is destroyed or unmounted/sold the connection is again lost.
* player can travel between galaxies once per day at cost of 100B credits (two way is 200B, open for balancing)
- 5h mission: First contact with cyborgs after destroying 10 cyborg super-carriers in new galaxy,
Story: cyborg NPCs received a coded SOS Prejor signal from our galaxy - side result of manipulation with Prejor technology by Crimsons. Therefore the cyborgs invaded into our galaxy with goal to find and help their makers.
- 6th mission: Find the last remnants of Prejors which would proof that Prejors are makers of the races in our galaxy but they also left our galaxy long time ago = negotiate truce with cyborgs.

This truce would not include the handling of local fights = each new territory taken including new planets, base, base lvl up etc would cause attack from cyborgs - to test your capability to stand the position you achieved.
Each base would be possible to build stronger in new galaxy using Prejor tech (or it special modification as reward for disable super-carriers) = more space for ship modules and new boosted types of ship modules to the now known.
New galaxy with much more Exotic planets... and flooded by cyborg NPCs (Prejor origin)
Existing artifacts would work in both galaxies and players could take to the new galaxy only what is in their cargo our mounted on their ship.
New galaxy details open to suggestion, we have on forum some nice suggestion of new races etc. With design, I would like to ask the Artist guild to help Dan.


To be continued...
Spoiler: One universe has space for many galaxies and secrets. Although Strylls escaped their destruction, we managed to capture a part of their communication: "... Destiny needs new crew...."


Meanwhile the scientist discovered the way how to manipulate with stars and form stellar systems from solar systems. viewtopic.php?f=6&t=34441
(thus two new possibilities: create solar system.. and from 2+ solar systems form stellar system)

As to territories if you could "tow" your planet into them(2.5k energy?) +% def and att depending on # of legion members in territory guarding it

well, I would rather suggest to start from small steps:
1) solar system
2) stellar system
3) territories
4) galaxies
Just to see at each phase, how it is impacting the game experience and interest of players. I would assume, that solar systems and stellar systems would not have big negative response, really not sure about general response to territories.
The concept of galaxies is not finalized yet.

+1 Mojo...way to take a lot of disjointed ideas and make a platform for discussion.