We might not ever know what the end was going to be, since with the ending cutoff by WB and Mainframe not wanting to spoil the ending in a hypothetical season 5, I can understand why they removed hints towards to the conclusion.
That said, oof, yeah, summed up my feelings for the last 2 & 1/2 decades. One hand, IF they were going to address it later, especially with Megabyte back, then it's YMMV-bad-to-decent-to-great SET-UP for a possibley great conclusion and send off for him.
I always loved the very beginning of Season 4 where he's still training by himself for games, when AndrAIa catches him and tries to get him consider actually Letting The Frag Go and have a peaceful life. Between that, and the younger Enzo reminding him of his worst and best qualities he squashed down to survive, only to be "replaced" by his "better" version, while alot of townies view him as the "grim aggressor man", especially any brought back from back up without cloning blues, it's gotta be rough feeling like an "inferior" copy in the town he saved with only some being grounded to see that outside a musical number.
And yeah, I can't blame Hex and an emotional young Enzo ragging in him right before a heroic sacrifice. But man, as much as Matrix HAS been shown to have legit problematic prejudice to virus, killing them when they're down, he not only made the choice to stop that with the worst, Megabyte, he's getting called out by his flip flopping younger self who adores & hates him (boy that sounds familiar....) and Hex, who we all stand, but yeea-aah, girl did only "break good" after Megs captured her & started torturing her, which after she helped throw her great "love" to the web. Her heroic sacrifice in Season 4 was great, I got choked up, and it was heroic...but it's debatedly her ONLY heroic act in all 4 seasons.
The virus as a hated minority CAN work with ALOT work-as a metaphor for people with menal illness. Show virus who sneak in but don't cause problems outside bloody adds. Show a virus who isnt a light switch of chaos (we love you!) but may be stable.most of the time and hurts no one, but has mood swings where they consciously fight their user given impulses to destroy, successfully! And let some of them live!
(All of this is of course is still NEVER going to be a 1 to 1 with a real life groups, metaphors, let alone metaphors in a 90s kids show and all that.)
The best possible ending I could think of where be one where the cast, in the middle of action & a quadrillion pop culture references, confronts the fact they're all clinging to the past. Something they HAD let go of before, but now are back sliding. Dot's & Matrix's cloning to better days, while different with Dog rejecting the present, and Matrix hating & adoring both, is just 2 ways to doing the same thing, with hurting the rest, with Bob falling into the same trap for not.feelimg enough, because he's not his old self (I sense a theme!)
Maybe that's the reason Megs kidnapped lil Enzo at the end was Hex's gift to him was either a copy of herself like they did with AndrAIa, or if it's some of her code, maybe he gains virus abilities, even becomes a Virus / Guardian. Cue angst and distrust from Matrix, dramatic confrontation, shouting their hearts out angry boi style until they get to root that Matrix is neither hero Enzo thought he was...but he was NEVER the villain Matrix thinks he's is, he's still a hero and his fa.iky does love, and at least 1/2 the town. Hell, maybe it's either trusting his younger "better" self to be a "good" virus allows himself to trust, well, himself, be cause if unfinished beta prototype of a kid can be that great, shouldn't be, the latest model, be at least as good?
Cue Matrix distracting Megs long enough so Enzo can use his new powers to subtract Megs destructive qualities his User cursed him with, WITHOUT changing him from a virus, which hes stated before to be cruel & wrong to force someone to be different. This could be the fictional, computer way to let him be the real version of himself minus the destructive qualities masking everything, in a way that obviously has no relatable, direct analogue in real life, but again, virus don't really work a direct 1 to 1 to real life groups.
Thus "Enzo Matrix" has defeated Megabyte again, as their 2 separate selves embracing the good qualities they have individually and that they hate together, with some help from Hex from the grave to help her brother to move on as well (theming!)
.....and in here somewhere Dot & Bob reconcile, maybe Dot learning from her 2 brothers to move on and accept the present, maybe after Bob reveals something, like he can switch back and forth with glitch powers, they have a romantic kiss while hes in that mode to prove she can love the post war version of him.....and maybe they do this after a time skip to give them time, so they're not pulling this after Dot & 2nd Bob rushed a wedding, earn some good will for her from the audience.
That, or the unlikely chance we ever get a continuation, "reboot" (hah.) the final arc and put everything that was supposed to hint at the true finale in where it was supposed to go, instead of doing the extra work to clean up some of the contrivances from season 4.
I could go on and on, but this is a good as any place to stop. Stay Frosty, Sparky, and may everyone be alphanumeric!