It’s mostly the third semester plotline which imo is poorly written because, unlike the matrix, the villain has the power to actually rewrite reality. And yet, when the protagonists turn him good, he doesn’t start using his powers for good, fixing injustice, giving everyone (not just the protagonists) the power to shape their own fate… no, he just stops using those powers. The altered world is presented as a ‘false reality’, like in matrix, even though it’s clearly stated that it would eventually become real. It’s as if they took the core idea of matrix but forgot the parts that made it work in the original story