Hey! Yeah... I know it got a little complicated at the end... let me see if I can elaborate
Saffron was normal until Kokomo Island, where Emiko fried Saffron's mind to protect her friends. After that Saffron was put into cryo... But Sanny the Ghost, who was constantly following Emiko around in hopes of getting back to her monolith on Ovok, found Saffron's "empty" body, and decided to "borrow" it for a while.
Not long after Kuzzter and Geschosskopf were taking Saffron/Sanny back to the KSC, but when they flew over "ground zero", where the krakens devastated Baukenbaur, she "felt" all the back ground radiation, which she considers "positive energy"... this is how she originally died of radiation poisoning in @Geschosskopf's OP Travelling Circus. Anyway, when she picks up all that wonderful "positive energy" she gets this crazy idea of starting her own religion to worship her monolith, and jumps ship...
Yeah... that completely backfires and causes a mass panic... and at this point Sanny, along with Saffron, cops an attitude with the "stupid unenlightened kerbs", leave Saffron's body and head back to the KSC to find Emiko... and come up with another way for her to get back to Ovok.
But then Saffron's body also shows up back at the KSC... only now the Handmaiden is possessing it... which means she must have homed in on it right after Sanny left it... and also must have left Bruberry's body, which she was previously possessing, out in the desert where Geschosskopf and his recruit find her a little later on.
Now how Badie fits into this is her body died on Earth, yes, but her spirit endured, and held onto the Kraken handmaiden spirit with everything she had... like having a ghost trying to strangle another ghost throughout eternity. The inspiration was from a TOS episode called "The Alternative Factor". This is why I kept saying the handmaiden was "insane"... She was constantly fighting off Badie in her mind.
So when the Laytheans, along with Emiko, Chibi and Thompberry, finally vanquished the Handmaiden from Saffron's body, all that was left was the soul of poor, shattered, Badie... who needless to say is extremely messed up and confused.
Not gonna lie... it was all just a very complicated way to bring Badie into the kerbal end of the story, and try to make it semi-believable.
As for the Empress and Emiko... my idea was yes, the Kraken's thought of Kerbals as primitives... But Emiko was a feisty primitive, who kept standing up to the Empress and trying to fight back even when the odds were totally against her... In many ways this impressed the Empress, and she started growing fond of this little insect. And in the end the Krakens came to realize it wasn't really Emiko or Chibi, but the Laytheans who actually took the handmaiden down.
And the Laytheans were part of the Hive, which we only learn about at the end... and really don't know what exactly it is yet.
What we do know is this whole time the Krakens apparently thought Emiko and Chibi, being so closely associated with the ET's, were totally under their control. But in the end they learn their error... Emiko and Chibi and the rest are NOT of the Hive... Kerbin has NOT been absorbed... which changes everything. Yes, the Krakens still want revenge... but they realize now they were aiming at the wrong target this whole time.
Platy-people and insectoid screenshots were from Spore, yes. Kraken and ET warship screenshots were from "Sins of a Solar Empire".