Here's a theory of the Origin Of Zexal and where did it come from since we don't know how Zexal came to be but I think this theory might help:
As we know Zexal is when Yuma Tsukumo, protagonist of the Yugioh Zexal series, overlays himself with Astral, the being from Astral World sent on a mission to find his missing memories which were split into 100 number excluding the over-hundred numbers.
If you don't remember or don't know what the Zexal form is here's a video where Yuma and Astral zexal morph for the first time:
There are two other Zexal morphs that they do which are different than the first so here's Zexal Morph 2 and 3 but skip to the 1:51 time stamp in the 3rd video.
Alright so now you know the three Zexal morphs/forms here's what I think the Origin Of Zexal is:
After defeating Don-Thousand was defeated by Astral and sealed away then later the seal being broken making Don-Thousand able to be free, Astral gained a power where if he fused with someone, that person being Yuma Tsukumo, they would form Zexal. How he obtained this power was when he defeated Don-Thousand and before being sealed by Astral some of Don-Thousand's power Astral managed to obtain. To sum things up if those who don't understand what I said Astral obtained a power to Zexal morph after defeating Don/Thousand sealing him. The 3 forms of Zexal however were obtained differently than the first one since the other two were obtained during their duels in which they did the Zexal morph for the second and third time.
But that's just a theory and what I think the Origin Of Zexal would be if it was mentioned in the show. If you have any questions or you don't understand something then I'll answer your comments below. Please let me know in the comments below your thoughts on this topic and would you have liked to see the Origin Of Zexal in the show? Playmaker out peace!!!!✌️✌️✌️✌️