. And just remember, it is of course all fanfiction. Well, here we go. 
The arrival: Let's assume Rhys said to himself "Screw my search for Maia, I marry Lena" at the end of his quest and chose to return to his homeland with a certain obsessive girl. Furthermore, Nial takes the hand of the beauty he rescued from prison, Aliar. Aron finally defeats Dark Force, maybe he falls in love with the woman his father rejected (that must be awkward) and in the end, the Alisa III flies through a black hole, travels back in time and arrives in the sol system. So far, so good.
The betrayal: Now let's talk about the twist. We never know what happened after the Alisa III makes contact with Earth. Here my idea starts (disclaimer: I took some inspirations from some fanfiction I read many years ago. But I don't remember where I read it so I cannot give you any link, sorry). Earth invites the former people of Palm to land on the moon and welcomes them. Of course, as we all now, the Earthmen are an antagonistic force in PS so their welcome won't last long. They gather information about the Algol star system from landing the aliens. Maybe by talking to the people of New Mota or investigating some of the ship's data. Keep in mind, the Earthmen are technologically advanced and we assume Earth is already dying, so its people are desperate to find a new home.
Alisa III becomes Noah: So after getting all the information they need, the Earthmen betray the people of the Alisa III, kill them or imprison them. Using the technology, parts and engines of the salvaged Alisa III, the spaceship Noah is constructed and the Earthmen "set sails" to Algo. Keep in mind, we traveled back in time so history will repeat itself to a certain degree. Any Palman is either killed or left to die on the doomed planet Earth.
The android: However, there is one survivor from the Alisa III. None other than our beloved Mieu. Or Wren. Either androids will do. I will continue with Mieu since I guess she can hide her synthetic identity better than Wren. Aron gave her a final mission: Infiltrate the Noah, reach the Algo star system and prevent the dark future. Let's assume she just can't kill every Earthman on the Noah so she has to find another way to save Algo.
Many, many years later we arrive in the Algo star system. During the construction of the mother brain, Mieu tries to sneak out. She steals a small shuttle to travel to Palm. Unfortunately, the Earthman notice her escape. Noah's cannons fire laser beams at the shuttle and one hits it. The shuttle crashes on Palm and Noah's scanners reveal that there are no signs of life in the wreck. What they don't know: An android was piloting the vessel so there were no signs of life in the first place.
The mysterious android: When the people of Palm discover the wreck, they find Mieu heavily damaged and basically shut down. Nevertheless, after a certain amount of time they are able to repair and reactivate her. But her memory took severe damage from the crash and so her words make no sense at all, she basically acts like Miun (kind of ironic). The Palmans decide to put the project on ice for now since there is no way to get anything useful out of the android.
Mieu reborn: When Mieu wakes up once again, she is already on the Alisa III. As far as I remember, the game's lore states that she was constructed after the war between Orakio and Laya (?) so for now we assume the war is over. The Orakians, who love creating machines and cyborgs, decide to reactivate and reprogram this ancient relict which the Palmans brought on the Alisa III to investigate it at a time before the names Laya and Orakio were a thing. During her reconstruction, the Orakian scientists are able to base Mieu's personality on the remains of her old personality. Even her purpose to serve Orakio is surprisingly easily integrated. Just her memories are gone. Or are they?
A chance to break the cycle: We are back at the end of Rhys' quest. Rhys is indecisive whether he should marry the girl he searched and fought for or the girl who risked her life to help him. So he asks for advice. Lyle is a bit of a jerk and no real help for him so he tries is luck with Mieu. In the previous timeline, Mieu told Rhys that marrying Lena was the more reasonable choice since marrying Maia would be considered as treason and also he would abandon his people.
When he asks her this time however, Mieu's memories are suddenly triggered. She sees images of a Lena's and Rhys' wedding, a giant explosion (Neo Palm), the screams of more than 10000 people, a black hole and more. She has no idea what happened and is really confused. But for some reason these images influence her. So she helps Rhys to make up his mind and tells him to listen to his heart this time. Which results in him choosing Maia instead of Lena. And now the events take a different course than in the previous timeline.
Sun instead of black hole: Ayn and his party eventually conquer Azura after defeating Siren so this place becomes the new home of the people of Cille and Shusoran. Ayn marries Sari. I don't like the idea of him marrying Thea who is his distant cousin. In a way it is nice that he fulfils the promise his father couldn't do. So his family and the kingdom of Landen are reunited.
While Dark Force and the dudes in Lashute destroyed the Neo Palm tried to move the Alisa III in the black hole in the previous timeline, this time their focus is on Azura - for now.
Sari and Ayn are busy fighting Lune's army when a messenger from Azura arrives in Landen with grave news. Siren returned to Azura and massacred most of the Layans, including Thea. Few can escape, among them Rhys and Maia (I just don't want them to die). Siren also somehow manages to change the Alisa's course towards the sun. Of course, he is being manipulated and supported by Dark Force and Lashute. But: At least nobody is heading towards the black hole.
Start a new - into a promising future: During the events of Crys' adventures, more and more memories return to Mieu although she is still confused by them. For example, she recognizes Laya to some degree from the past, when Crys awakens her. So she hugs her very soon although she does not know why
. The rest of Crys' adventure continues like normal. After defeating Dark Force, the pilots manage to change the Alisa's course. On last piece of memory is triggered in Mieu. She recommends the pilots to investigate this star system. So the ship heads to the third planet of the system - which is Earth, now abandoned by humanity. After probably 2000 or 3000 years without humans, Earth had a chance to recover from the damage and is now once again a habitable planet. Mieu instantly remembers the blue planet and now she is able to unlock most of her former memories. The Alisa III is heading to a new home, maybe even being joined by the Neo Palm (I mean, why not?). The party watches the sky while the ship is approaching Earth, maybe Crys is holding Laya in his arms (or rather warrior Kara? Who knows). Mieu closes her eyes, being at peace with herself, knowing, that her mission is finally complete and that Aron can now rest in peace. She won't tell anybody of her memories though - there is no need to burden these people, who already suffered so much, with the misery of the past. With the destruction of the Profound Darkness in the distant Algo system, Dark Force as well is finally history - even here on Earth/Alisa III.
So what do you think of my weird theory? Unfortunately, the game never tells us why Dark Force never tries to send the Alisa in the Black hole in Crys' or Sean's questline. I guess the Layans on Azura made him really mad for some reason. I wish I came up with another significant decision for Mieu to make during the 3rd or 2nd generation. But I think the idea of her being a critical part in a timeloop and thus basically playing PS III twice
was not too far off. 
