There are 5 versions of Children of the Atom, the first 4 of which were only released in Japan. The main way to tell which version you are playing is by looking at the title screen, as the version number is shown on there. Version 3.00 is the latest version, and was the only one released in America and Europe. Out of all of these different versions, version 1.00 is the most interesting, as it has several differences:

Version 1.00	Version 2.00 and later
In version 1.00, a couple of the messages shown during the intro were changed in later versions. The actions the characters perform during the intro is also different between versions.

Version 1.00	Version 2.00 and later
The intro plays out slightly differently in version 1.00, lacking this screen, and the above screen has a single-colored background. Later versions changed the background, along with the placement of some of the characters -note that you can't see as much of Wolverine, Storm, Silver Samurai and Magneto as you can in version 1.00.

Version 1.00	Version 2.00 and later
Version 1.00 does not have the amount of wins per player on the high score screen. All later version have this info.

Version 1.00	Version 2.00 and later
One small quirk with version 1.00 is that several of the messages that appear on the screen are displayed in the middle. In later versions, they were moved up slightly. If you beat an opponent during a sudden death round in version 1.00, the "FIRST ATTACK" message will appear on screen. In all later versions, this message does not appear. This also means that during sudden death games, you do not receive the first attack 10,000 points bonus in later versions. You still get it in version 1.00.

Version 1.00	Version 2.00 and later
The bonus points text displayed after the round is over is spaced differently in version 1.00. It was spread out more in all of the later versions.

Version 1.00	Version 2.00 and later
In version 1.00, finishing an opponent with a hyper X move displays the words "SUPER FINISH" on either the left or right of the screen, depending on which player got the super. In later versions, the text appears in the upper middle.

Version 1.00	Version 2.00 and later
In version 1.00, the number during the combo counter is slightly higher than it is in all later versions. Version 1.00 also has the "pts" text next to the points you get for combos above the life bars, later versions lack this text.

Version 1.00	Version 2.00 and later
After a two player match, version 1.00 lacks the medals beneath the winner's score, which later versions have -these medals mark the number of times a player has won a game in a row. The colors for the continue text and number, along with the word "SCORE", is different in version 1.00.

Version 1.00	Version 2.00 and later
After winning in arcade mode, version 1.00 has a different colors for the "WINNER", score numbers and "INSERT COIN" text than later versions have. The hyphen in the win quote is placed slightly lower in version 1.00 than it is in later versions. This also happens anytime a hyphen appears in the ending texts.

Version 1.00	Version 2.00 and later
On Wolverine's stage, version 1.00 only has a few dinosaurs appear in the background one at a time here. In all later versions, big herds of them run together.

Version 1.00	Version 2.00 and later
You can continue to attack your opponent after a round is over by pressing the start button. If you do this in version 1.00, it will cause your opponent's stun gauge to change colors -eg get worse, so you can pretty much stun your opponent with one hit by the time the second round actually starts. Note on the above left shot, Iceman's portrait box has a red background. The later versions fixed this by always having the stun color reset to blue before the round begins.

Version 1.00	Version 2.00 and later
Storm's lightning storm attack is colored differently in version 1.00, later versions changed the lightning color to blue. In version 1.00, this attack stays on the screen much longer, so it can do more damage and hits than in later versions.

Version 1.00	Version 2.00 and later
If you pick Gouki and lose in version 1.00, Gouki is not a black silhouette at the continue screen, whilst he is in all other versions. Another difference is that in version 1.00, Gouki still gets continue tips like all other characters -this was dropped from all future versions.

Version 1.00	Version 2.00 and later
In version 1.00, one of Magneto's fists always glows with energy when he moves towards and away from his opponent. In later versions, this was removed.

Version 1.00	Version 2.00 and later
In version 1.00, Magneto's EM Pulse move only shoots one stream of energy -in the later revisions this move has three streams.

Version 1.00	Version 2.00 and later
One Magneto has been defeated, version 1.00 features Anne-Marie Cortez dropping down with the rest of the Acolytes. For unknown reasons, she was removed from all later versions. She seemingly helps Magneto up by grabbing his crotch -there are additional unused sprites of her that seem to suggest Magneto would lean on her to support himself. Her sprites are still in the later versions, but they go unused. During the above, version 1.00 does not have any debris falling down in the background. All later versions feature this. In version 1.00, when the Acolytes float down, this music plays. Then when your character leaves Magneto, this music will play and keep going on even when Avalon explodes. In all other versions, this new piece of music, which is not in version 1.00, plays when the Acolytes float down and will keep playing until Avalon explodes, where things go silent for a short time.

Version 1.00	Version 2.00 and later
In version 1.00, the text boxes for the above ending shot are at the top of the screen. All later versions move them to the bottom.

Version 1.00	Version 2.00 and later
In Psylocke, Silver Samurai and Wolverine's endings, these explosion effects are colored yellow in version 1.00. Later versions have them colored green instead.

Version 1.00	Version 2.00 and later
In Cyclops' ending, version 1.00 gives Professor X some dialogue. In later versions, his words were given to Colossus instead. This is really minor, but in version 1.00, Colossus' hand does not overlap Jean's hair. In later versions, it does.

Version 1.00	Version 2.00 and later
In Storm's ending, Forge flies slightly higher up in version 1.00, leading to his head being overlapped by the text box. All other versions have him fly lower, so this doesn't happen.

Version 1.00	Version 2.00 and later
During Spiral's ending, this one text box is placed too high up in version 1.00, and is cut off. No text appears in it either. This was fixed in all other versions.

Misc differences

Intro/demos

-Version 1.00 is missing this screen, which was added to all later Japanese versions -it appears before the intro starts.

-During a demo fight, at the character select screen, version 1.00 is missing the info about the automatic guard, which later versions have.

-In version 1.00, during a demo fight, the CPU picks characters as soon as the character select screen appears. In later versions, the CPU will highlight a few different characters before selecting.

-During a demo fight, the characters do not use their intro animations in version 1.00. In later versions, they do.

Gameplay

-Sentinel's hyper X move works differently in version 1.00. You can't charge it, but Sentinel will always release three energy blasts. In later versions, you can keep pressing punch buttons to charge it up. You then have to keep pressing punch buttons to release the other two blasts.

-Generally speaking the difficulty of the CPU opponents is lower in version 1.00. This is especially noticeable with Magneto, who is much more difficult in later versions.

-Juggernaut and Magneto both have the same ko grunt in version 1.00. In later versions, they have unique grunts.

-Juggernaut and Magneto's ko grunts often won't be heard in version 1.00, this was fixed in later versions.

-In version 1.00, whenever Magneto changes the background, it moves anti-clockwise. This also happens in version 2.00, but in all later versions, the background moves clockwise.

-In version 1.00, if Magneto beats you with a perfect, he'll say some Engrish: "you are beaten, Magneto is scream!". He was meant to say "Magneto is supreme!". In later versions, he will instead only say "you are beaten!".

-If you lose to Magneto and use a continue in version 1.00, you have to fight Juggernaut again! This was most likely a glitch, as in all other versions, this doesn't happen.

-Whilst it's possible to fight Gouki in version 1.00, it doesn't seem possible to play as him -I can't get the code to work. If you hack the game he is playable and works fine, although there's a continue screen difference (see above) and his ending has no text (see below).

Endings

-The amount of time a text box is displayed on the screen varies greatly between versions, generally speaking.

-During Sentinel's ending, version 1.00 lacks this text box, which all other versions have. However, version 1.00 does have this text box, which all other versions don't have. The sound effect for Master Mold taking off is the same as what the other Sentinels have in version 1.00, later versions changed it to a unique sound.

-Starting from the part where Jean appears, Wolverine's ending does not play any music in version 1.00. Later versions have this track play when Jean appears, and then this track when Wolverine finds Silver Samurai.

-During Spiral's ending, from the part where she goes to Mojo, version 1.00 has this track play for the whole scene. In the later versions, an extra track, which was not in version 1.00, was added, and plays first. Then this track plays second.

-Gouki's ending does not have any text displayed during it in version 1.00. In later versions, this text is displayed.

-Version 1.00 does not have the credits -the music is in the game, but goes unused. Later versions will show the credits if you beat the game without using a continue.