Three months after the previous game, a new criminal organisation known as Gospel is on the rise which created a powerful virus. Lan and MegaMan.EXE now must stop them.
This game introduces the SubChip system. They can only be used outside of battle, but provide useful functions such as healing, unlocking locked mystery data, or altering the encounter rate. It also features Style Changes, the first of the transformation types used in the series. Style Changes can alter MegaMan's elemental affinity and Charged Shot and provide passive effects in battle.
Other features implemented in this game include the alteration of the Custom Screen, improvement of the Add function, and introduction of the wildcard *-code to make combos easier to execute.
This game provides examples of:
- Adult Fear: Lan's trip to Netopia. First, his money is stolen. Then, after arriving in Netopia, he gets into a stranger's car, getting his battle chips stolen. After this, he has an argument with Megaman, tosses his PET on the floor of his hotel room and storms out. This gets his passport stolen. After getting everything back, he attends the ONBA conference in Netopia castle, when suddenly the castle's traps activate and everyone is dumped into the dungeon filled with deadly traps.
- Battle Rapping: A very out of place one occurs in the airplane scenario. See the "Radar" page for details.
- Bragging Rights Reward:
- Hub Style blends this trope with Infinity +1 Sword. The unlock requirements involve S-ranking every boss except Bass, after which Hub Style becomes your next Style Change result. It has the effects of all four Styles rolled into one and then some, and is without doubt the strongest Style in the game. However, you have little left to use it on, barring rematches with Bass.
- Beating Hard Mode (detailed below) bestows your original save file with the Sanctuary chip. By that time, you're probably good enough that you won't need the assistance of a defensive field chip.
- Chekhov's Gun: Right outside Lan's HP is a purple mystery data on an isolated platform. You eventually gain access to it in the postgame, and it contains the ArmyData for the SS Licence. You have to pass through the WWW Area to get there, which begs some questions.
- Darker and Edgier: Though only to an extent, the game's villainous organization Gospel attempts to commit multiple acts of rather violent terrorism compared to what Wiley committed (if you ignore the plot involving a bunch of car crashes which was glossed over), which includes bombings, attempting to destroy a dam to flood a public park, crashing an airplane filled with passengers, and unlike Wiley, Gospel takes a more violent approach to their minions who fail them (such as when they blew up the Starter Villain). There is also a slight uptick in profanity.
- Escape Battle Technique: This game is the first to implement using the L button to escape from battle. It still retains the Escape chips which offer no chance of failure. Later games fully embrace the L button as the escape command and discard the Escape chip from their libraries.
- No One Could Survive That!: Up to Eleven and straight into Artistic License Physics territory. Lan should have been dead from radiation poisoning before Battle Network 3 if he was exposed to hundreds of thousands of rads, even with a top-notch radiation suit. Then again, this is some kind of wacky computer-born radiation that not only causes someone to walk sideways when he tries to go forwards, and starts merging the real and cyber worlds if left unchecked, so perhaps the usual rules don't apply... In game, it is said to be magnetic radiation suggesting that it affects iron in the blood at a molecular level instead of an atomic level.
- Not Rare Over There: One NPC asks to be paid in "Guard *" chips. Talk to another NPC, and she'll give you 30 of them.
- Numerical Hard: Getting 100% Completion in this game and inputting a certain code at the title screen unlocks Hard Mode. The only difference in there is that enemies have increased HP and damage; they will cough up the same rewards as your usual game.
- Old Save Bonus: Retro Chip Traders let you get chips from the first game if connected via Link Cable.
- Party in My Pocket: Used briefly during the Okuden camp scenario. Since this is the only time in the series it's used, it's very jarring; apparently players were just expected to know what it meant when all the other kids walked into Lan. (Standard Battle Network procedure when Lan's in a group is just to have everybody hang around somewhere, checking things out, until you trigger a cutscene that moves the party.)
- R-Rated Opening: The first arc is very much this. The game starts with a man flat out gassing a young girl with intent to hold her for ransom, showing no remorse for it, and then, he is implied to be killed in a You Have Failed Me moment.
- Sequel Hook: The scene after the end credits, in which Dr. Hikari suggests that someone was manipulating the leader of Gospel. That the Bonus Dungeon is named WWW Area doesn't help.
- Unwinnable by Mistake: You can't jack out of QuickMan's stage once you enter. Jacking out is the primary method of restoring HP, and it also cuts you off from accessing better chips, making getting stuck here very possible.