The reason why Hacker is evil is that he himself was infected with a sentient virus that altered his behaviors to go against his original purpose and instead try to harm Motherboard and take over Cyberspace. It's one of the reasons why Motherboard, nor anyone else for that matter, but mainly Motherboard and Dr. Marbles can't trust Hacker. They know the truth and that it's not their old friend. It's the virus talking, and that whatever he says is only under an ulterior motive to take over Cyberspace. For all Motherboard and Dr. Marble know, their old friend is good and gone.
He likes to think it was entirely his choice to go against Motherboard, but he has less free will than he thinks. Actually, he has hardly any free will at all for that matter, and is basically a puppet for the virus. The virus itself could not harm Motherboard nor make a virus that could, though it could infect others lower than her, so why not infect someone else to infect Motherboard in a roundabout way?
There is some evidence to suggest this in the episode "The Grapes of Plath". We see the Crab Prince infected with a glitch that turns him into a compulsive liar. The cure from the glitch is a bath in the titular Grapes of Plath from the Fountain of Truth. The Hacker mis-hears this as the Fountain of Youth, and he dives into the bath himself. Afterwards, his personality is altered temporarily. He wishes the Crab Prince a happy birthday, and then asks to have either a pony or a lollipop for his own birthday. The only information we are given on the Grapes of Plath is that they can cure negative conditions like the glitch that causes compulsive lying. This suggests that there is something external that caused The Hacker's Face–Heel Turn.
This is also suggested by the episode "Inside Hacker". Matt is shrunk and sent inside The Hacker's body to replace the memory chip in his H-drive (Heart Drive?) to turn him away from evil and back to his original self. This =Cyber Squad= performed this plan with Motherboard's supervision and approval. This suggests that they all believe that The Hacker is not acting like his true self.
Most of the time when measurement comes up, cyber- gets prefixed onto the names of the units. The same is true of lots of other things in the series, but they're mostly cyborglike in appearance, and there's no real way to do that for units. It stands to reason that something else makes these measurements Cyberspace-specific.
In the first episode of the show, "Lost My Marbles", it's established that "hardly any time passed" while the Earthlies were adventuring in Cyberspace. That seems like they're confident some time has passed, but it's little enough that they wonder if it was All Just a Dream (until Motherboard and Digit contact them again).
The idea is that yes, they were away for a very short time as measured in the real world. While they were in Cyberspace, time was moving more slowly for them. These are different universes, so it seems possible that time would work differently in each, and you can fit more Cyberspace time within real-world time. That is to say, a cybersecond is defined so as to feel like a second to a visitor from Earth, but it's actually a fraction of the time.
Spatial measurements also use the cyber- prefix, like the cyberfoot and cybermeter. My assumption is that space is also more compact in Cyberspace, although the spatial dimensions could also be scaled larger than in the real world. The dimension between the portals is the "vortex", and maybe it's a funnel-shaped one that properly changes the size of objects traveling between the universes.
This theory has a lot of other fun ramifications. Depending on what the ratio is for the flow of time, it explains episodes like "The Snelfu Snafu" where the Earthlies stay in Cyberspace for days on end. Going the other way around, we can imagine that they're called into Cyberspace often, explaining why they don't age much (ignoring the holiday episodes), but ages go by in Cyberspace between their visits. How does Hacker get out of some of the wild situations he's in at the ends of episodes? Aside from the cartoon logic, he just has a lot more time to work with than the Earth kids might realize.
"Hugs & Witches" takes this to its logical conclusion. It's possible that Cyberspace only started to exist with the invention of the Internet, and time has been more compact so its history can play catch-up with the real world, but it could also be some mathematical world that has always existed alongside the real one. This episode has a character named Lady Ada Lovelace, and if she is meant to be the historical figure living in Cyberspace, it implies the latter. How is she still around? Apparently, once she got into Cyberspace, she invented Time Travel.
The episode involves Buzz and Delete trapping Dr. Marbles and Lovelace inside her time machine, which will send them back to the beginning of time. At the end of the episode, the tables turn, and Buzz and Delete are later seen being tormented by a dinosaur. If they were sent to the beginning of time, they've already been through 14 billion years of history, with dozens of millions left to go before they return to the present. That's bad enough, but what is 14 billion real-world years in cyberyears? In other words, Buzz and Delete, the oft-misguided "duncebuckets", have lived orders of magnitude longer than the universe as we understand it.
Another troper mentioned on the YMMV page that the new episodes don't start with the kids in the real world being pulled in by Motherboard as much anymore. Instead, the kids tend to already be inside Cyberspace at the beginning of the episode. Then, they stumble upon The Hacker's plan of the day.
We know that the cybersites that are infected by the Mean Green get a green filter placed over them. It also appears that the process of infecting a given site with the Mean Green is custom-tailored to only impact the native residents of that site. We see this when Jackie and Inez go to the unnamed jungle cybersite, and the Mean Green impacts the native gorilla population, while leaving the CyberSquad untouched. We see this again when Matt and Digit go to Helping Hand Land, and the Mean Green impacts the titular Harriet the Hippo, while again leaving the CyberSquad untouched.
While Motherboard herself is patient zero for the Mean Green, Control Central is not turned green. If the site had been totally infected, it is likely that Digit would have been infected. He was created there, and he considers it to be his home. It is unclear whether this would have infected the kids as well. They are not native to Cyberspace, but a much later episode, "Hackerized", proves that they can be infected by purpose-built toxins from cyberspace. If any site could be considered a home for the kids, it would be Control Central, as they only got pulled in to help Motherboard. It's also likely that they would be there to help Motherboard, which gives Wicked every reason to custom-tailor the infection of Control Central to target them.
We see The Hacker arrive in Shangrila and threaten to remove or destroy the Good Vibration relic. He claims that this will cause the cybersite to turn into the most disgusting place. Master Pi gives himself up very easily, and he seems more interested in applying the golden drop test to Buzz and Delete. Additionally, the soldiers make no effort to stop The Hacker from stealing the relic, and they actually help him maroon the CyberSquad on the island surrounded by whirlpools. At the very end, Matt actually removed the Good Vibration relic from the top of the pyramid to stop The Hacker from stealing it, but nothing changed. Then again, after The Hacker almost falls off the pyramid, the relic is suddenly back in its usual spot, so there is a continuity error on that point.
This is supported by the episode "The Borg of the Ring", where The Hacker uses The Totally Rad Ring to wish for Shangri-la's Good Vibration to become 'bad vibrations'. We see him destroy the relic while Master Pi and the soldiers look on, but we never see Shangri-la destroyed or transformed.
The episode starts with Matt already inside The Hacker's body. It is revealed that the kids dug up an old shrink ray that Doctor Marbles built awhile ago, and they used it to shrink Matt. Jackie, Inez, and Digit are guiding him with a model that shows The Hacker's insides. Their goal is to put a new memory chip into The Hacker's H-Drive, which will turn him from a bad guy into a good guy. This plan to forcibly rewrite The Hacker's personality definitely raises some ethical concerns, whether we are going with the theory that The Hacker was turned evil against his will by some outside force or not. It seems very out-of-character for Motherboard to approve of such a plan. However, Motherboard doesn't appear until the very end of the episode, where they need to get the robot to the Northern Frontier to rescue Matt. This suggests that the whole plan may have been thought up by the kids, who might not understand the ethical concerns. They then executed the plan without Motherboard's approval. Once things went wrong, they approached Motherboard for the first time or help. Of course, Motherboard wouldn't take the opportunity to scold them yet, as her priority is to save Matt.
