Liked the twist, actually. While it's true that Missingno is treated more as a joke meme, the way you used it here feels fitting to the entire "chaos" theme going on:
Missingno is a glitch, it corrupts the game its in when it shows up. So what would that look like in-universe? Like the end of the world and everything going up in flames.
So yeah, I'd say you nailed it. I also like the idea of Unown being linked to odd happenings in the world. While I feel that their exposition was a tad too direct, I think they managed to come across as mystical...which I believe was the point, right?
The one thing I feel was a bit off was Cynthia. Not in the idea of her not wanting to try hoping for a solution...but more that I feel like it would have fit a bit better for her to come across as...I guess more angry or cold than outwardly scared? And let me be clear: I don't mean that her being afraid is the issue (I actually think it fits, considering the scope at play here) but more that her SOUNDING overly scared feels a tad off since...well, she's Cynthia XD
...either that or have Teejay admit to feeling a bit more scared than he sounded. Either could help XD
Still, I liked the general direction this went. Looking forward to what comes next!
P.S: What happened with Melanie though??? I know that Teejay BARELY won their pokemon battle, but we didn't really get to see her reaction or Teejay's final word on the matter or anything...kinda left me a bit confused, I won't lie.