This sounds like ReBoot, a Canadian computer-animated series that ran from 1994-2001. It's a show about life inside a computer, as Bob the Guardian defends the citizens of Mainframe against various threats, including viruses, web raiders, and most importantly of all, incoming games.
Assuming a few squishy memories owing to your age -- kindergarten at the time -- this sounds like a solid match. I don't have any photos to upload at this moment (though the IMDB link has some), but I'll explain why I think it matches.
I remember watching a cartoon about a group of teens (maybe young adults) fighting monsters in special zones that popped up at random in their home town. They fought by either thinking of a weapon/armour/abilities or writing them down in a notebook (don't quite remember) and then proceeded to save the day. I'm pretty sure the zones disappeared after each battle and that each of them was unique.
Bob the Guardian, along with the various denizens of Mainframe -- but usually Dot Matrix, her little brother Enzo, Enzo's dog Frisket, and a few others -- would typically find Mainframe's integrity threatened by the schemes of resident viruses Megabyte and Hexadecimal, as well as the biggest threat: incoming games run by the user. These games were huge, purple-ish, glowing cubes that descended from the sky and locked a portion of the city and all inhabitants in its path into the game until it ended. Bob and company were tasked with successfully defeating the User in each of these games, because a loss meant that the portion of the city beneath the game would be corrupted and destroyed, and all citizens trapped within converted from conscious people into slug-like creatures called Nulls. Should the user win too many games, it was possible that Mainframe itself would be destabilized and destroyed. At the conclusion of each game, the glowing cube would retreat into the sky and vanish.
Bob and company accomplished their task within the game by clicking the icons on their chests and saying "Reboot!", which granted them powers and equipment of the various NPCs and other characters in the game.
I think they were all trained by an organisation, because I remember one episode where a reporter goes into one of the special zones along with a new recruit and the regular heroes and gets separated, only to be saved by said recruit.
Bob the Guardian is a member of the Guardians, specially-trained sprites who are sent to all computers across the 'Net to protect and defend their denizens from all the bad things out there.
In regards to the reporter portion: Mike the TV -- a recurring comedy sidekick character, and literally a TV with a mouth -- was Mainframe's reporter and was pulled into one of the games at least once, in the episode "Wizards, Warriors, and a Word From Our Sponsor."
Enzo eventually became a Guardian trainee and he did indeed prove crucial to winning his fair share of the games. (Thus, satisfying the "new recruit" bit of your description.)
Through the course of the cartoon they found out about the guy who is the root of all evil, built a spaceship and started travelling through space, time or some weird dimension to find him. The crew was 3-4 of the teens and a teacher. The exterior of the ship was that of a normal (water) ship.
This one is a looser match, but I'm going to chalk it up to "Maybe you're misremembering some details due to your age at the time." Season 3 of ReBoot took a much different turn from the previous seasons' self-contained "game of the week" episode format, and introduced a season-long plot where Bob, Enzo, AndrAIa, and Frisket had been lost to the Web and were trying to return to Mainframe, which was currently (somewhat) undefended from the resident viruses Megabyte and Hexadecimal.
Megabyte, as a virus, definitely qualifies as a "root of all evil", as his previously "safe kind of dangerous" schemes from previous seasons turned quite serious. He would openly infect any uninfected citizens he could get his claws on, turning them into loyal recruits for his army. Megabyte was set upon capturing the Principal Office, the control center for all of Mainframe and Megabyte's ticket out of Mainframe and his way to infect the entire Net.
During this season, Bob, Enzo, and AndrAIa (re)encountered Gavin Capacitor, the Crimson Binome, a stereotypical pirate captain and crew who sailed the Web on a stereotypical Age-of-Sail-style pirate ship, and adventured with him and his crew for a while as they searched for a way back to Mainframe.
It aired around 1999-2000 in Bulgaria (most likely it was from the mid 1990s), which is when I watched it. It had quite a few episodes, maybe even 2-3 seasons, because I remember watching it for a good year, maybe two. I remember it being quite dark from time to time and having to increase the brightness on the TV.
I don't know how to check 25-year-old Bulgarian TV listings, but I will say that the original broadcast dates for the show do indeed match this timeframe, being 1994-2001. The show proper had 3 seasons (1994-1995, 1995-1996, 1996-1997) and two direct-to-video movies released in 2001.
Although it's a highly ancillary match, some of the episodes were certainly dark in color and probably would have benefitted from bumping up the brightness on TVs of the time. :)
I can't say for certain, but I think it was a 3D animation, similar to that of Beast Wars: Transformers:
The animation style of both ReBoot and Beast Wars: Transformers were highly similar, considering the same studio (Mainframe Entertainment) animated both! :)
This is a few years late, but hopefully this is a match, and you'll get to re-experience a really fantastic show! :)