One day, Gemini accidentally happens upon some records of Alpha's lying around, detailing the "Day of Liberation". Instead of reprimanding his Lieutenant for snooping, however, Alpha decides its finally time to tell him of the day he became the Commander of the M.S.I...And of Commander Zeta, his mentor.
It starts as most origins do...With a home devoured by flames. A lone Goomba is surrounded by fire, his existence threatened by the presence of a towering shadow.
Confused, forgetting everything he ever was, the Goomba can only accept death.
Suddenly, the shadow comes under fire by a plethora of weaponry, as a Koopa wearing a trenchcoat comes in to perform a daring rescue.
Only able to buy themselves enough time to escape, the Koopa carries the Goomba away to his copter, and returns to his home base...
The Goomba awakens inside a medical ward with two giant metal arms attached to his sides. After struggling to get up he examines his surroundings and then has a talk with the Shy Guy doctor over the intercom.
He learns where he's at, the M.S.I. Base, and finds out that if he wants to learn more about his arms he should find the person who rescued him up on the roof of the base.
The Goomba uses a map in his arms to find the Koopa looking out at the sunset. The Koopa humorously greets him and then tries to assess how damaged he is right now.
The Goomba explains the pain he feels and the emptiness inside of his memories. He then asks about the monster he saw, hearing from the Koopa that he is Balroc, a Koopa Tyrant that has spread devastation unopposed for years now.
He had been attacking a Goomba settlement because it housed traitors, and that's where he found this Goomba at.
Despite knowing that his family or friends might be dead for good, the Goomba isn't perturbed, because he doesn't remember them anymore.
The Koopa finds his lack of fear intriguing, and says that maybe this was meant to be, like his father used to say.
The Goomba then wonders if there's any way they can stop this tyrant. The Koopa can't believe he's hearing this from the Goomba after how short of a "life" his memories have given him. The Koopa keeps pressing him further and further, testing the strength of his will to fight.
The Koopa even cites the story of the Four Heroes who fought the Shadow Queen, saying that maybe in this era, the people need something like that again to bring them hope.
The Goomba insists that he wants to stop the tyrant and avenge the people he's tormented, saying nobody should have to experience the fire like he has ever again.
The Koopa readily agrees and decides to take the Goomba as his protege, giving him the new name Alpha, and finally introducing himself as Commander Zeta. Zeta wants Alpha to see him as an equal, but warns him that the journey they're about to embark on will be a difficult one.
For in order to defeat the tyrant Balroc, they're going to need to hunt down the legendary power of the Elemental Overlord...
The next morning Alpha and Zeta head on foot for a long trip to Toad Town, wanting to avoid the detection of Balroc's "Doomships".
Upon arriving in town they meet up with a human named Fernando, who turns out to be Mario and Luigi's dad, though Alpha doesn't know it at the time.
They then head to the Osagi Woods, where Zeta shows off some of his technology, like cloaking devices and night vision goggles, to help them get around the labyrinth and avoid fighting the Outer Guardian.
Zeta starts imparting lessons to the doubtful Alpha to help boost his confidence a little. A very important piece of advice he imparts is to be careful at all times, especially when things seem easy.
They then disarm the traps in the castle with a lighter on Zeta's person and make their way to the stone, where, upon touching it, activates the Inner Guardian.
Zeta takes the titan on while Alpha freezes up, traumatized by memories of Balroc's titanic shadow.
Zeta calls out to him in confidence, saying that he can absolutely do something to help, even if he thinks he's weak.
Alpha's confidence goes up slightly and he tries to use some of Zeta's advice to call upon a powerful ionic cannon from his arm, incinerating the Inner Guardian in one strike.
Thus, they claim the first stone.
Alpha has to rest up a bit in Toad Town after the recoil from the cannon damaged his back a little. Meanwhile, Zeta reports the success so far to Fernando.
Fernando hands him a watch and tells him its to better keep track of time instead of doing his usual quirkiness. Zeta thanks him and afterwards, him and Alpha head to the docks to go for the next temple.
Alpha learns how to discern important people among the many Toads and after I. the foreman Zeta has him clear the other Toads out so they can work.
Alpha and Zeta then piece together how to open the way underwater to the temple, but worry that the big split in the sea puts them on a time limit for the next patrol.
After narrowly avoiding the Outer Guardian they head inside and solve the puzzles before confronting the Inner Guardian. This time though Alpha's not able to muster up the strength to contribute as much, leaving it to Zeta's bag of tricks to win them the day.
Zeta then warns Alpha of getting overconfident, because he needs to concentrate properly in order for his arms to function at full power.
Back in town the two run into a conundrum. The next temple is near Nimbus Land, but due to the current war climate the Nimbusians are taking a neutral stance and thus not allowing anyone who aren't their own to enter the city.
Alpha suggests a transforming device to disguise themselves but for once, Zeta is unable to provide the solution.
That's when they encounter a younger E. Gadd, who after exchanging a few helpful words gives them his prototype Duplighost Cloak so they can enter Nimbus Land.
The two decide to implement their plan next morning. While Zeta disguises as a Nimbusian to get on the Nimbus Taxi, Alpha will use his cloak to get on undetected.
This works out with one close hiccup, and they make it to Nimbus Land in record time. But from there the two have to figure out the trigger to enter the temple since questioning the people would arouse suspicion.
Once that's done they have a run in with Skyus, the Outer Guardian, who noticed them cloaked thanks to movements in the air.
But he doesn't force a fight, seeing how he doesn't want to doom others to become an Outer Guardian should they beat him.
Thus the two are able to move through the temple to eventually fight Fujin. Alpha freezes up again, forcing Zeta to shake some confidence back into him.
Ultimately this results in Alpha and Zeta managing to use their skills together to put Fujin down. But Fujin laughs at the futility of their journey, as they are not the ones destined to succeed, and no one, whatsoever, has claimed all seven stones before...
With that haunting message in the back of their minds, the two leave the temple.
They then have the Taxi Driver take them to the island housing the Lightning Palace, following a slight bribe on Zeta's part.
Zeta warns how their cloaks won't work on the Outer Guardian here, given the presence of electricity. So instead Zeta resorts to a tranquilizer dart to knock them out, pitying that this had to happen to his brother.
Alpha questions this and finds out that the Outer Guardian was once Zeta's brother, now inflicted by the Outer Guardian curse. Zeta and his brother were defectors from their parents' indoctrination, but his brother disappeared one day while Zeta went on to create the M.S.I., naming it with the same initials as his brother's full name.
After this important tale, the two go through the temple's traps and face the Lightning Djinn in a game of chess. The two manage to win without having to sacrifice one or the other, and claim the next stone.
They then take the taxi to Moleville so they can head towards the Terra Cave.
Zeta explains to Alpha how he manages to pull out so many weapons and tells him that he might want to consider making that a feature in his own arms someday.
Zeta then uses an EMP grenade to disable the Outer Guardian so they can enter the cave safe and sound. After thwarting the few traps available they activate the Inner Guardian of the stone, Drill Golem Onyx.
Alpha and Zeta's teamwork continues to grow stronger, and they manage to best another guardian. But before they retreat into the stone, Onyx warns them that they'll never be able to gather all the stones, as one person keeps intercepting the heroes who gather them outside the final temple.
If they want to learn more, they have to go ask the guardian of the Frozen Palace.
Zeta is antsy to get right to the Frozen Palace, which even Alpha notes is strange behavior on his part. Zeta says they're so close to getting the power to stop the tyrant that screw it, let his Doomships find them. He's ready to send a message that Balroc's reign is soon to come to an end.
So Alpha and Zeta trek through the harsh desert sands through heat and cold and eventually climb Shiver Mountain to reach the Frozen Palace.
The two expertly evade confrontation with the Ice Golem, but Zeta says that the golem should consider himself lucky that they have obligations to fulfill, otherwise the golem would be dead for what he's done.
They then make it to the end of the temple and encounter the Inner Guardian, a human by the name of Lord Kelvin.
They learn from Kelvin that a green-skinned witch is responsible for what's happening, and that seems to unnerve Zeta a little.
Kelvin forces them to fight despite his due respect towards the two for making it this far on their own. Alpha hesitates less and less as the fight goes on, leading to him landing the finishing blow on Kelvin.
Kelvin remarks how he wishes the two well, putting his faith in that they will be the ones to not succumb to the witch's machinations.
Zeta immediately wants to go to the final temple, despite Alpha's warning that he is pushing himself too hard. Zeta's manner of speech is also becoming a little more forceful and desperate.
They take a long walk to the Nova Cesspool, where Zeta makes increasingly obvious attempts to get Alpha to retreat to no avail.
Alpha picks up that Zeta's worried about the witch, and Zeta says that he just doesn't want Alpha to lose his life again after "dying" once before.
Alpha refuses to leave his side through thick and thin, stating how its because they work so well together that they're able to succeed.
This renews Zeta's sense of courage and they decide to press on through the Nova Cesspool...Only to quickly be intercepted by a familiar laugh before being thrust through a portal of darkness.
Unnerved by the dead sights around them, the two press on through an abandoned spaceship and eventually find records detailing how the crew of this ship was killed by black creatures with yellow eyes.
Alpha's mind tells him to run and run, but his body disobeys at every turn, pressing forward with Zeta into the realm itself.
Zeta comments how this place shouldn't exist, and warns Alpha to keep his guard up.
The two leap off the ship and have a run in with the black creatures in the video. But they are pulled back...by the command of one Cackletta, whom Zeta recognizes by name.
Cackletta argues her goals with Zeta for a little bit before casually dropping how she had a hand in Balroc's rise. He was always a monster but...she simply nudged him in the right direction to gain ultimate power.
Zeta doesn't care what she's done, he plans to beat her and escape this realm to finish the tyrant off.
Cackletta laughs, stating that war never ends. Good and evil will always be locked in an eternal battle. But not to worry, he will be freed from the cycle by her hand, and fed to the Heartless.
Cackletta locks Zeta in a magic cage with her and the two fight as Alpha can only helplessly watch on. But, surprisingly enough, Zeta manages to stand on even ground with the witch for a time.
Until Cackletta reveals, however, that she's been holding back, and starts thrashing Zeta around the arena with utter ease.
But Zeta suspected that she wasn't using all her tricks, and took advantage of her arrogance to plant traps around the arena that activate on his command.
Wires suddenly thread through Cackletta's entire body and suspend her in place. Zeta, now in control of everything but her heart, forces her to activate a spell that will allow him and Alpha to escape.
Then he blows her up, ensuring her defeat...Or so he thought.
Cackletta revives and immediately lashes him brutally with lightning until he's barely able to stand, cursing him out all the while.
Zeta, in his weakened state, realizes just how insignificant he was at the very end. That he was nothing but a pawn in a bigger game...
But in his final moments he turns to the tear-ridden Alpha and tells him to stay strong, that he is to be the seed that'll bear the fruit of hope for the next generation.
Zeta hands Alpha his trench coat and tells him to run, but not before pulling one last weapon for his pockets.
"Now go, Commander Alpha" Is the last thing Zeta says before turning to Cackletta and arming his last weapon...A Holy Hand Grenade.
The explosion wipes out Cackletta again and all the Heartless in the vicinity while Alpha, shaken and barely able to stand, rushes back into the ship to find the portal Zeta opened for him.
In the process Alpha loses an eye to the Heartless.
Emerging on the grassy outskirts of Toad Town, Alpha watches as the Elemental Stones he had gathered are forced back to the temples with Zeta's passing.
Everything they did meant nothing. Cackletta won. And Balroc still reigns.
...Alpha refuses to let this be the end they want though. To honor Zeta's memory, he drags himself back to the M.S.I. Base, saying he has a lot of work to do.
In the aftermath of these events Alpha adopted the title of Commander without hesitation and got to work adapting the hyperspace technology from Zeta's coat into his arms.
Then he learned how to build new weapons to boost his arsenal to the point that not even Balroc would stand a chance of beating him.
His chance to prove his worth came when Balroc was heard being sighted in Toad Town. Alpha rushed to the city and found it consumed in flames, much like his old home.
But now he didn't see a titan in the shadows. Balroc was nothing more than a giant, pathetic, scaly beast.
Fernando, his wife, and his two kids Mario and Luigi are sent through a portal to somewhere safe thanks to the Star Spirits while leaving Alpha alone to fend off the Koopa tyrant.
In a battle that lasted a long, long time, Alpha throws everything he had at Balroc to try and put him down. This was to be a battle that would be remembered, even if the savior was not.
Ultimately Alpha killed Balroc by overloading him with energy until he exploded, upon which he collapsed to the ground in exhaustion, only to be saved by his new allies in the M.S.I.
With this story now over Gemini has some thoughts to share in the present. He says he has a stronger respect for the burdens Alpha put on himself but Alpha doesn't want any pity for it.
He just did what was right, and continues to do so even if others might not agree with it.
With this story over Alpha heads to the roof to pay respects to Commander Zeta's grave.
Unknown to him, he's being watched far, far away by someone who intends to make him pay for forgetting him...
Alpha Gaiden END.