Space Invaders
The Professor appears in a secret location and states that the area is desolate but is close enough for human contact. Meanwhile, Abigail informs General Morden that the aliens have arrived and tells him that she has a plan. Morden allows Abigail to carry out her plan.
Meanwhile Marco, Eri and Tarma are looking for the POWs when their helicopter is attacked. They manage to land and repel the attack, and free a POW. The P.O.W. tells them that while they were battling the Rebel Army, the Space Army came and abducted them. The three make their way to the Rugname, but fall into a trap and are captured by the Professor. Marco wakes up after a short dream where MS-Alice speaks to him. The Professor is excited to meet Marco but leaves to examine Tarma and Eri's memories. Marco breaks free and finds the Professor examining Eri's memory, who plans to use her memories for an unknown purpose. Tarma frees Eri and the two find Marco. The Professor sends the Rugname after them, but is defeated. He states that it is time to go and leaves with Marty. Marco tries to save the prisoners but is restrained by Tarma.
After the incident, Eri states that they managed to rescue 15 of the 26 soldiers. Marco is upset that he was unable to save everyone.
Secret Ending
Tarma and Eri find more prisoners in the secret base, and free one of the POWs. The POW has a dream about protecting his family. Tarma notices Eri cry, which results in her almost killing him as a result.
The Sand Kingdom and the Golden Hero
Eri is in the Arabian ruins. She is surprised to find that the Pharaoh is not around, though it is due to Beatriz defeating him in "The Pharaoh Treasure". Eri notices military footprints on the ground and follows them. At the end, she reaches a large rebel base under construction and Abul Abbas overseeing the work. An Arabian soldier informs him that Assy Nero is low on fuel and reminds him that it consumes a lot quickly, so Abul has the soldier radio headquarters for more fuel. He suddenly smells Eri's presence in the room and orders his soldiers to chase after her.
Rebel soldiers chase Eri, where she rides a camel and prepares to fight them. Eri finds herself outnumbered but suddenly a robot suit appears and drives off the Rebel forces. The man inside the suit tells Eri to lower her weapons. When he reveals himself, the two recognize each other through their nicknames. They properly greet themselves and El Dorado takes Eri around the town, where he is praised by the villagers for driving away Rebel forces. El Dorado explains the town's plight to her and requests to come along to stop the rebels. Eri, not wanting to decline such an offer, accepts his request.
Abul Abbas is later informed of the news and battles El Dorado and the Regular Army but is defeated. He continues to fight despite obviously losing until he is informed that Assy Nero is ready for action, so he leaves. Eri and Fio pursue Abul while El Dorado temporarily leaves to grab something. In the new tunnel, Abul deploys Vita, who sends out devastating laser attacks which could cause the whole tunnel to collapse. El Dorado brings in a Slug Gunner, which surprises Eri as she thought he stole it from the base. El Dorado simply replies that he had acquired and taken good care of it. Vita fights Eri in the Slug Gunner but is defeated. Vita is about to explode when someone calls her, overriding the self-destruct sequence and leaves.
The three chase Abul Abbas, where he is informed that Assy Nero has been refueled. He sends the giant drilling machine at them, only for it to be destroyed in the ensuing battle. Abul calls headquarters, and is responded back to by Abigail. Abigail shows displeasure with Abul being reckless and damaging Assy Nero, so she has the rebel soldiers take all of the equipment back. She also tasks Vita to recover the core engine from the wreckage. Abul begs Vita to save him, but Vita takes a higher priority over the core engine and leaves Abul. Abul begs for mercy, but El Dorado is not forgiving towards him for harming his kingdom. Eri allows El Dorado to do whatever he wants with Abul, and later departs with Fio.
Secret Ending
The Back You Can't Reach
Roberto Nicola is a new recruit in the Regular Army, and is commended for his hard work by Sophia. Sophia assigns him to work with Fio, which he is excited with. She later has the two transport a new weapon from Junior Engineer Midori.
On the way, Roberto notices a girl by the side of the road and tries to help her. However, it is a trap, and her bodyguards apprehend Roberto. Fio recognizes her as Beatriz, but she runs off with the cargo after freezing Roberto and many soldiers. Fio waits for Roberto to thaw out before reminiscing on how to deal with the situation.
The group decides to stay at a nearby motel. Allen Jr. and his men kill Regular Army sentries and are confronted by Roberto. Roberto manages to hold his own against him, but is eventually defeated. Allen Jr. prepares to finish him when Fio appears and drives him off. Fio helps Roberto back on his feet, before asking him to accompany her back to the motel because she is scared of thunder.
The next day, Fio, Roberto and the others try to find the stolen cargo when Beatriz ambushes them with falling rocks. They repel the assault, forcing Beatriz to retreat; the Regular Army pursues her.
At the Rebel Army base, Allen Jr. is angered by the fact that Beatriz led the Regular Army to the base. The Regular Army arrives, so Beatriz takes a controller from Allen Jr. and deploys the Cabrakan. Fio is surprised that they would be carrying such a weapon. Roberto does his best to damage the weapon, but gets wounded battling it. Beatriz is about to finish him off when Fio appears with the Thunder Shot. After a long battle, the Cabrakan is destroyed. Beatriz laments that she will die without seeing her sister again before being brought back to reality by Allen Jr., who forcefully drags her away to escape.
At the Regular Army base, Sophia commends Roberto for his actions and introduces him to the rest of SPARROWS.