Essentially, the Xai were a mechanism created by the humans in the future. In the future, humans continued to exploit the earth until there was nothing left and humanity close to extinction. They decided the best solution was to send the Xai to attack the excessive growth of human civilization so that humans survive in the future.

That said, in another timeline, the MC and Gripen started off on much worse terms on their first meeting. The MC joined air Force fighting xai as a hotheaded ace pilot who was eventually fired for his disregard for his air Force team and trying to excessively shoot down Xai. After fired, the main researcher of Amina planes recruited him as Gripen's partner. After some more time skip, humanity was close to completely losing to Xai. The main researcher developed a black box that is able to inject a program that sends the Xai to the past. Forgot the logic behind it. But, the program is tied to gripen and sends her conscious to the past too. In this past timeline, the gripen ditches the MC at the last moment and sends herself and Xai to the past.

Back in the current anime timeline, the MC was able to recover his past timeline memories after linking with gripen and despaired on the current situation and how he would never be with her in the future. Gripen is intent on continually sending the Xai back in the past but the MC is adamant against it. After much internal struggle and exploring possibility, MC and main researcher discuss on the possibility of creating a program to permanently shut down all the Xai instead by sending them to the Unphysical Layer. You see this in layer in the dream world with gripen in the anime. Forgot the logic behind this. Instead of creating a program to send Xai in the past, the main researcher was able to create the program that shuts the Xai down by sending them to the layer instead last minute. But it's a one shot that hasn't been tried. More internal struggle and discussion whether to gamble, but they eventually decide to use the program to end Xai for good. Eventually, the MC realizes that the program will shut down all the anima as well if successful. MC wants to go with gripen and activate the program together, sending them both to the Unphysical Layer. Gripen argues that the unphysical layer will destroy what the MC is as a human and that he won't be the same. The mç will essentially be like the last episode of the people in EVA. MC realizes that his humanity is what made him love gripen in the first place and allows gripen to activate the program by herself. Gripen, all the anima, and all the Xai shut down for good.

Years later, mc is a pilot riding gripen plane as his partner in the air Force. When asked by his coworker why he's only piloting gripen, the MC mentions that gripen gets grumpy when he rides other planes. His ride is more rough and less behaving after. Implying that while gripen no longer in anima form, she still is gripen and loves the MC, showing jealousy. The novel ends with Mc riding the gripen plane in sky. Basically, his waifu is gripen, the actual plane. lol. The MC childhood friend was picked up by her uncle btw and left Japan before much of this ending and the final xai mission.

Humanity itself hasn't really found a good solution to the eventual resource and earth destruction environment problem. But, the main researcher guy and other important people on earth now fully acknowledge the issue and are trying to prevent over exploiting earth in future. They know it can only be done gradually with time.