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I have got the Moreya from the asteroid base and have to make the decision as to who to take it to. Any advantage with either. does it affect the plot line in any significant way?

If I already have a Moreya from the TER plot then I usually choose to surrender the newer one to TER and get the Katana instead. There isn't much in it either way, although you can get more firepower onto the Katana for pest clearance.

One advantage I can think of, if you got this ship early game, and dont change its weapons it comes in handy for stopping Haille running to the Terrans to blab about your actions.
Depends what decisions you take in the Yaki plot. But if you chose to lay the Nav beacons to earth leading the Xenon that way, Haille will then transit fast in his Kuraokami using travel drive through gates all the way to the Terrans. Stopping him you have to be lucky with any other weapon, but the beam weapons on the Moreya plus its speed are easier to give him a poke and break his travel drive .. Only problem you have then is you also need a ship to immediately teleport to which is a bit more substantial versus his Kuraokami .
Its a bit of an unfair mission imho, chances of stopping Haille on your first go are slim. It needs a prior save to re-do and plan the intercept.

I did this complex mix of missions again recently and chose to "Save them from themselves" = A lot easier, and once Haille has talked to the Yaki rep afterwards and convinced her the Yaki are in a better position, you still get the Yaki lockbox caches, and Haille as a 5* pilot plus his nicely modded Kuraokami.

So really .. You do you. Depending what choices you made, and which ship you would value the most afterwards.
I still go for Boso and getting the Litigious Rodent Moreya, its purely an aesthetic thing for me, I dont like the look/feel of the Katana and the Moreya with its cool looking paint job is more of a trophy ship for me, also nice as a scout exploration ship after its modded.

Boso: you can get Kat's anytime - rodents are more difficult to come by.

Moreya from the plot = unique ship with nice painting, what i remember. Also it will take a while until you can buy the blieprint/more of them.

Katana = normal Katana, you can buy a lot.

Something to note is with the Katana, you can carry more mines. That means more shenanigans with 1 shotting xenon capitals from cloak mode while you can.

Moreya from the plot (Lutidious Rodent, or smth like that) isn't unique, sadly. As well as Gumption's Gambit (just Kuraokami) or Raven Prototype. Geometric Owl is unique due to its special ability, but since it lose that ability upon finishing the relative quest - appeared as usual Moreya too.

There are quite a few really unique ships in game. And all unique vessels have their own separated chassis - see their distinguished Model strings in Information tab:
- Okinawa Research
- Hydra Regal
- Astrid (well, 2 of them and as far as I remember u can order another in case of all were destroyed)
- Earlking (rebuild if destoyed, btw, I have 2 in my game, but it is not intended)

Moreya can drag Minerals with loot Magnet and xen ignore it during the Plot.
If you ever planed to rebuild a Xenon Presents in some system, otherwise Moreya is more difficult to get at that plot stage Katana only costs a few cr.

I think there is finally an answer with 7.0 beta.

If you finish the plot the answer is Katana because it can destroy the amplifier easier, if that is your path. The Litigious Rodent has a better paint job for hangar sitting.

If you instead use these ships to farm Xenon Hs, then Rodent is superior. It holds more than 1 marine, which you can only use 1 at a time anyway, plus it is much faster. It can also equip burst rays to destroy the engines/turrets of the H if desired. Just don't do the amplifier part, or really you don't even need to dock with Yaki, so you keep the camo until you start the boarding process. I recommend Terran engines for boosting away.