The two games have similar plots, but as they each go along the differences start to show. Both of them start out the same: A new worldwide robot soccer tournament is started and Megaman sets out to arrest Wily before the event even starts to make sure that he doesn't mess with the event like he did last time, however, an announcement is made saying that due to underfunding the tournament can't continue, when suddenly Mr. X, the REAL Mr. X that Wily impersonated in Megaman 6, appears and decides to fund the tournament.
As he signs the paperwork Megaman meets up with his personal assistant, "Madame Y", who says that it was her idea to fund the tournament, as she's a big fan of the games, however, strange things start happening around the tournament and Megaman, joined by Light's robots decide to join to investigate what's going on, however, what they don't know is that Protoman has secretly assembled his own team under the guise of "Breakman" in order to help Megaman out and that Wily has given Bass the mission to using his robots to win the tournament and use the cash money to get better robot parts.
Halfway through the tournament, Dr. Wily, Light and Cossack are kidnapped and soon after Mr. X finds that almost all of his money has been robbed, but they can't put off the tournament as the stadium is taken hostage by the mysterious enemy, who traps everyone in it in a dome and forces the player character to fight through his last 8 robot minions and against the other playable characters, once that's all done, the player character finds that the 3 Doctors were still inside the stadium all along, just trapped in a hidden underground facility below it, however, when they leave the underground facility they are ambushed by Madame Y in a giant mech, who reveals that she was behind everything and that she kidnapped the 3 Doctors to build her a mechsuit to take over the city and that she robbed Mr. X to afford robot parts for the mech itself, and just for fun she decides to challenge the player character to one final soccer match.
The player character, at first, can't defeat the mech, however, all of the Robot Masters and the other playable characters give him the strenght to kick the ball with a supercharged kick, destroying the mech's outer armour and weakening it, allowing the player team to defeat it in a soccer match, and while at first Madame Y seems to not care about her loss and attempts to escape, she finds that the soccer match was a distraction made so that the 3 Doctors could make a trap to full disable the mech and catch Madame Y, saving the soccer tournament and the city.
After the event, the player character is rewarded with a huge cash prize, and what happens after depends on the playable character:
Megaman decides to spend the money on fixing up the robots that were damaged by the bosses and Madame Y, and spends the rest on a big party for his family and robots, even Protoman is invited but he abruptly disappears, leaving Megaman to host it on his own, until 6 robots, "DJ Man", "Bond Man", "Express Man", "Multi Man", "Scratch Man" and "Barrage Man" steal all of the food and decoration! And so, Megaman sets out on another journey to save the city from Robot Masters.
Protoman uses the money to upgrade his Proto Buster into the Hyper Proto Buster, giving him incredibly strenght as he disappears and sets out to find "Darkman", Madame Y's right-hand man who escaped and is still missing, Protoman finally discovers the location of his secret hideout and jumps into action! Finally, Protoman catches Darkman but he breaks his Hyper Proto Buster, forcing him to use his old one, which he uses skillfully to destroy Darkman. However, after the fight, Protoman realizes that he doesn't need the Hyper Proto Buster to be strong and leaves it on the ground as the hideout collapses and he escapes.
Bass returns to Wily's Fortress and is asked by Wily to hand over the cash prize, however, he reveals that he doesn't have it, and that shortly after winning it he left it in the desert, where it was buried in sand, Wily gets mad at Bass and asks why he'd do such a thing but he only responds by telling him that all along he only cared about winning the tournament to prove his strenght, not for the money. Wily gets even more angry at Bass and yells at him to leave his room as he gets out the blueprints for a new, more powerful and advanced robot who highly resembles Zero, as he says that he won't need Bass anymore after he is completed.
The gameplay in general is similar to Megaman Soccer (a standard soccer game basically) combined with the stats and other mechanics of Inazuma Eleven but in-depth:
Story Mode is special, in it you have to battle against 4 teams based on Robot Masters from the classic games in any order you like and after beating them the captain of the opposing team joins YOUR team, allowing you to use their abilities (this mirrors how Megaman copies the Robot Masters' abilities in the original games, allowing him to use their abilities), normally each opposing team consists of the captain being a Robot Master and the other members being enemies from their stage with maybe one or two other Robot Masters similar in nature.
In Story Mode, you can choose to play as either Megaman, Protoman or Bass, each one comes with a preset team of 8 Robot Masters as well as 3 characters, each captain plays slightly different from the others but the biggest difference comes in how their team plays.
Megaman's team consists of: GutsMan, IceMan, ElecMan, CutMan, FireMan, BombMan, TimeMan, OilMan, Auto, and Roll.
Protoman's team consists of: StrikeMan, CommandoMan, BladeMan, PumpMan, SheepMan, SolarMan, ChillMan, NitroMan, Enker, and Ballade.
Bass' team consists of: MetalMan, BubbleMan, WoodMan, AirMan, FlashMan, CrashMan, HeatMan, QuickMan, Sniper Joe, and Punk.
After defeating 4 opposing teams you have to fight a boss, these work like normal matches but often times the captain of the team (in other words, the boss itself) will use cheap tricks, such as Proto Eye jumping sporadically around the field trying to crush you and subsequently stun you.
While Hyper Bomb Edition and Lightning Bolt Edition have different playable characters, the player character teams in the Story Mode remain the same regardless of the version, what changes in Story Mode are the teams fought and some of the bosses.
Matches themselves work similarly to normal soccer matches in sports games, the players pick a team captain and form a team, then they select where in the field to place each member of the team and then they start the match, where they use the left joystick to move around while using the right one to aim in realtime, they use the 4 triggers to slidetackle, kick the ball, pass it, and the game's unique aspect: use their skills.
Each character has their own set of skills, for example, Megaman's default skill normally is the Mega Buster, which can shoot 3 bullets before having to wait a second, then it's able to shoot another 3 bullets, and similar to the main games it can be charged for more power, however in combination with other button inputs it can change slightly, pressing the Mega Buster button while kicking the ball will make Megaman turn into his Mega Ball form from Megaman 8 and kick the ball into the air, and charging and releasing it in combination with the slidetackle move it can make Megaman use the Charge Kick which extends the range of the move but slows down Megaman for a bit afterwards.
If that wasn't enough, stats can be increased throughout matches by by getting goals, dodging opposing teams and using skills to attack the other team, as well as performing "team actions" such as passing the ball to a faraway player, catching a ball that a friend throws or even slidetackling an opponent in order to help out your teammate, and if you and your teammate coordinate their skills at the right timing at the correct distance, if they're compatible, they can do a "Tag Attack", which can be really powerful and just like in the Inazuma Eleven games, is quite flashy.
you can use more combos and even charge up "Special Blasts" which can be devastating if used correctly, so skill is rewarded with more abilities which allow more advanced play.
In the game there are 6 stats based on Inazuma Eleven stats: "Fire" (Attack), "Wood" (Defense), "Quick" (Speed), "Shadow" (Technique), "Guts" (Strenght), and "Mega" (Special), and while they can be upgraded through special training minigames in Story Mode similar to like the original games, during normal matches everybody starts with their starting stats but they can increase them during very brief "Focus Periods" after each Goal via the methods described two paragraphs above this one, though they can also be used to power up skills which allows you to use more combos and even charge up "Special Blasts" which can be devastating if used correctly, so skill is rewarded with more abilities which allow more advanced play.
A slightly Mario Strikers-esque concept introduced in this game original to both Megaman Soccer and the Inazuma Eleven series are Items, but they're not as destructive as the ones in Mario Strikers, instead they focus more on just being helpful utilities, these items include "Rush Jet" which, when activated, causes the player to mount Rush Jet and dash forwards uncontrollably for 2 seconds or until the player taps the button again, this item can be used to push back opponents; another item is "Tango" which rolls up into a ball and dashes around the field, it can't be kicked by opponents but it can be kicked by the team of the player who summoned it, and if they kick it Tango will be sent in the direction it was kicked in at full force, and if it crashes into an opponent it will slow them down drastically temporarily and take the ball off of them if they have it.
Fields, just like in Megaman Soccer, belong to the different Robot Masters and are themed after them, however, in this game there are also fields based after Robot Masters not playable and Wily Fortresses, and while fields are the same in shape and structure, fields often have special mechanics that differentiate them from the rest. Hyper Bomb Edition and Lightning Bolt Edition have only 4 fields in common, the rest are completely different depending on the version and the only way to play a field from the other version is to play multiplayer with someone who does have that version.