Sada, whose expertise lies in natural sciences, gets approval to set up a lab in Area Zero to study it. She forms a team of other researchers, one being Professor Turo who has expertise in engineering and computer sciences. And at first they don't get along, especially with Sada more interested in the past while Turo is more focused on the future. Still, they're professionals and study Area Zero for a year, their research leading into the creation of the Tera Orb & control over Teralstallization.
Having accomplished this major achievement, most of the other researchers decide to leave to do work elsewhere, leaving only Sada and Turo. Having appeased the research backers for the time being, Sada refocuses her efforts on unravelling Area Zero's mysteries, especially of the Paradox Pokemon described in Heath's book. Slowly but surely, Sada and Turo start to grow close as they discover, while their goals couldn't be any further apart, both are just as passionate about their research as the other's (and both are a fan of Heath's research). They get into a relationship and soon Sada is pregnant. At this same time their research is coming up empty, Sada wishing she could bring forth the Paradox Pokemon from the past. Turo, now better understanding the Tera Crystal's power thanks to Sada's research, believes he can build a Time Machine. Thus they decide to combine their goals together: utilizing the Tera crystals, they'll build a Time Machine to bring ancient Pokemon forward to the present to create a better future! And it works, they bring forth their first ancient Paradox Pokemon, Koraidon, at the same time as Arven is born. For a while they live happily together, raising Arven and using the Time Machine to bring forth ancient Paradox Pokemon.
However the backers, who are unaware of the Time Machine and Paradox Pokemon, start demanding to see results for their funding. Sada starts feeling pressured and gets completely engulfed by her work with the ancient Paradox Pokemon; getting into fierce arguments with Turo and causing them to neglect Arven. Eventually Turo has enough and takes Arven with him back to civilization, leaving Sada and Koraidon (though he doesn't realize Arven has Koraidon's Poke Ball).
And NOW we change things from the game.
Turo leaves Arven with his parents (Arven's paternal grandparents) and eventually goes back into Area Zero to try and get Sada to see reason. However, by the time he gets back, he find Area Zero crawling with ancient Paradox Pokemon. He finds Sada, except there's two of her now! The real Sada, angry at Turo, explains she used his research to build a double of herself, Sada AI, and tells him to leave. Heartbroken, Turo is about to leave until Sada AI approaches him and asks for help. At the increased rate Sada is bringing forth ancient Paradox Pokemon, they'll overwhelm the barriers of Area Zero and escape all over Paldea which would be disastrous. Sada AI is unable to convince Sada of the danger and is prohibited from adjusting the Time Machine, thus she needs help from Turo.
Turo agrees and Sada AI sneaks him to the Time Machine. But instead of decreasing the rate of ancient Paradox Pokemon being summoned, Turo has grown disgusted of the ancient Paradox Pokemon so instead starts summoning forth future Paradox Pokemon, and the first one he gets is one that can take Koraidon head-on: Miraidon. More and more future Paradox Pokemon swarm out into Area Zero and get into territorial conflicts with the ancient Paradox Pokemon. Sada, confused on what's happening, goes to the Time Machine to see Turo and Sada AI. Furious, Sada commands Koraidon (who has been following her around up till this point) to attack them, but its reluctant to do so. However Turo's Miraidon takes the opportunity to attack Koraidon, causing both Paradox Pokemon to fight. Sada rushes to the Time Machine's control panel and tries readjusting it, however Miraidon ends up tossing Koraidon at her. Sada is crushed and the Time Machine is damaged, Sada's copy of Heath's journal also getting destroyed.
Koraidon flees as Turo recalls Miradon back into its Poke Ball, he tries to escape with Sada AI but Sada AI says she needs to repair the Time Machine. Turo, overcome with grief, decides to dedicate himself to dealing with the ancient Paradox Pokemon by using the future Paradox Pokemon. Meanwhile, Sada AI is able to fix the Time Machine, but now its summoning both ancient and future Paradox Pokemon (at a slow rate, but the overwhelming the barrier problem is still a upcoming issue), and without a copy of Heath's journal (with Sada's destroyed the only one that can be used with the Time Machine is Turo's copy that he left with Arven) the Time Machine can't be stopped. In addition, Sada AI feels a hidden program activate in her incase Sada was ever to die: the Paradise Protection Protocal.
While the protocal is inactive at the moment, she's worried once active she'll be too strong for anyone to go against her. She also needs Turo's journal, but doesn't know where it is, and Turo has gone crazy forming a future Paradox Pokemon army to wage war against the ancient Paradox Pokemon. Sada AI decides all she can do now is bide her time, so forms an ancient Paradox Pokemon army to go against Turo's. During these few years Koraidon is running and hiding, but it's being constantly hunted by Miraidon. Eventually Koraidon, using all its power, breaks through the Area Zero barrier and flies as far as it can into Paldea... but Miraidon has followed it.
AND now we get to the anime proper. Somehow Liko, Roy, & Dot get involved, befriend and help Koraidon, Arven gives them Koraidon's Poke Ball as he wants nothing to do with it much to our heroes confusion, and they go on adventures. Meanwhile, in addition to being hounded by the Explorers, Miradon also appears every so often trying to kill Koraidon (not sure how but they could maybe figure out a way to have the Explorers, probably Amethio, team-up with Miraidon).
Like in the games, Arven once ventured into Area Zero and his Mabosstiff got seriously injured and needs to get the Herba Mystica; which of course Liko, Roy, & Dot help him with. This is when Sada AI gets in contact with them and says she needs their help, but both them and Koriadon need to get stronger in order to do so. Like in the games, after finding the final Herba Mystica, she'll contact them but this time Arven overhears and Sada AI asks if he has his father's journal, which he does and she tells them all to come to the lighthouse lab, much to Arven's irritation.
At the lighthouse lab she tells them she needs them to come to Area Zero with the journal as she can't leave until they do. Now at this point not sure if they'll need to get Penny and Nemona involved, Dot is just as much as a tech wiz as Penny and Liko and Roy should have gone through enough character development that they're both strong battlers now (not to mention they'll also have Arven and Dot). Then again, I can see the story developing where Dot and Liko from a strong friendship with Penny and Nemona, respectively, and bring them along for the extra help. Sada AI would also likely request they come without any adults knowing, so no Friede or the rest of the Rising Volt Tacklers.
Getting into Area Zero, with how I set things up they could do several things now that's there a war between ancient and future Paradox Pokemon going on. One thing they could do is the group getting split up, one continuing their way to Sada (I'd say Liko & Dot (& Nemona); and they'll have Koriadon whose hiding in its Poke Ball) while another are found by Turo (Roy & Arven (& Penny)). And of course Miraidon has also followed them back.
Skipping to meeting Sada AI, she tells them what happened (meanwhile Turo tells the kids he find his version of the story) and that the real Sada is dead. With convincing from Arven, Turo brings the kids reuniting them and agrees to a "truce" with Sada AI to stop the Time Machine once and for all. As they place the journal into the Time Machine, the Paradise Protection Protocal activates and they need to defeat the Sada AI and her team of ancient Paradox Pokemon. But once she's defeated Turo reveals he doesn't want to stop the Time Machine but use it to usher in a future of his design with his army of future Paradox Pokemon. Everyone battles and defeats Turo's initial team, but Miraidon reappears which gives him enough time to find the Poke Ball lockdown security system which locks all unauthorized Pokemon in their Poke Ball. All looks helpless until Sada AI reminds the kids that Koraidon is registered to Sada so can be used. And this is when we get the final Koriadon and Miraidon battle, Liko Terastallizng Koraidon helping it defeat Miraidon.
Completely defeated, Turo breaks down though has come to his senses. However the Time Machine can't be stopped as long as both Sada AI and Turo's Journal are there. Turo decides he wants to fix his mistakes, deciding to do use the Time Machine to travel to the past to try and save Sada; if not in this timeline than another. Koraidon and Miraidon settling their differences and deciding to go with the Professors, Turo and Sada AI take the journal and travel to the past, thanking the children (and telling Arven they're proud of him). And so everyone leaves Area Zero, having saved Paldea (Arven is devastated, but everyone cheers him up).
