高中二年级学生真夏大地在暑假开始前的晚上，在电视上目睹了种子岛上空突如其来的不可思议的圆形虹光。曾经见过这种虹光的大地内心汹涌澎湃，决定一个人向着种子岛进发。“父亲因事故而死亡的谜题”、“幼年时遇到过的不可思议的少女的记忆”等复杂思绪从胸口涌出。到达种子岛的大地因某设施的报警声而与“EarthEngine”相遇。“你就是队长吗…”伴随着询问声，大地看到的是从天王星袭来的谜之完全机械生命体“KILL-T-GANG”，少年的冒险也在这绚烂星空中拉开帷幕。

真夏在未经通报的情况下驾驶机器人“地球号”出动，基地众人惊讶中迎击“KILL-T-GANG"来袭，但是由于没有经过任何训练，遭受到了机械生命体的重创，这时博士紧急调用一神秘黑客侵入导航系统，间接控制住机体，辅助迎击。在黑客神秘声音的配合下，真夏大地终于击退来犯的机械生命体，并回到基地。在基地中，真夏以外的遇到了幼时遇到的神秘少年（岚彻平）与被他唤醒的神秘少女（梦塔花），只是二人的处境似乎并不太妙，而且真夏也将面临同样的处境。在方舟派针对迎击派的阴谋中，真夏将如何面对呢。

神秘黑客登场，居然是基地司令5年未见的女儿——夜祭明，并且似乎暴露了一段司令的糟糕私生活？自由了的彻平和花与夜祭明真夏一起住进了司令家中。几天后新的敌人来犯，方舟派的salty dog为了陷害真夏而向真夏透露来犯者是他的杀父仇人。本应被禁止出击的真夏在方舟派的怂恿下出击，然后还未维修的破败机体几乎导致全败的局面，就在真夏危机的时刻，彻平和花联手出动了，他们的真实身份到底是什么呢。

彻平救下真夏后被怀疑是KILL-T-GANG的一员而被隔离，真夏因担心彻平前去探望。与此同时，KILL-T-GANG的阿玛拉和摩柯伪装成卖可丽饼的旅行商人潜入并袭击了基地，确认了彻平的身份并试图带走他，彻平为了保护人类要跟他们离开时，真夏发动了能力，召唤了生命光线手枪并击败了阿玛拉。此行为也让博士和司令怀疑真夏、彻平与花和明之间似乎有奇怪的联系。

接触战之后，确定了彻平是KILL-T-GANG的一员Albion，也因此方舟派盯上了彻平。因为彻平在基地内被保护着，所以方舟派决定劫持彻平的基因提供者-岚英司。与此同时，司令给明和彻平派发了秘密潜入空间站将人工冬眠中的英司接回的任务。彻平和爸爸（基因提供者）的会面将会发生何等故事？他们又是否能够成功将英司接出来呢。

利用了天海道的混乱脱身的彻平的父亲英司至今下落不明。与此同时，状况无时不刻地变化着，为提防KILL-T-GANG的袭来，仅将被选中的人类送至地球外的“基沃特斯计划”不断推进着，“方舟派”谋划着将计划中所必须的的小花抢夺过来，而正当被派遣至种子岛基地作为监察官的広末正准备将小花带走的时候，大地匆忙而至正好赶上，并使出了得意的飞镖技将小花救了下来。

正如小花预料的那样，阿马洛特和摩尔金出现在第1防卫圈内。在被两面夹击陷入苦战中的大地面前出现的是彻平和他的KILL-T-GANG.Albion。将所有的迷茫都切断之后，彻平亲手破坏了自己的自主模块，在他的协力下，大地成功击退了阿玛拉和摩柯。并且，因为这次的战果，西久保宣布独立游击队“仲夏骑士”成立并指明大地为其队长。

除了彻平外还存在另五个设计试管儿。为了阻止其中一人——津的觉醒，大地一行向台场出发了。津在那里的一家赌场担当庄家。被友人孤立，对至今的人生都感到后悔， “到头来，这只手什么也无法抓住”。而出现在他面前的正是阿玛拉和摩柯，从摩柯口中接受作为游星齿轮装置的自己真正力量而觉醒的津的脸上浮出了蔑视一切的笑容。

游星齿轮装置的第五人是现役的偶像爱衣。乘上MachineGoodfellow.蛇花火的她让大地一行被迫陷入苦战。另一方面，阿玛拉绑架了小明并威胁她用骇客技术将低轨道上所有的冲击兵器全部停止，被赶上绝路的小明的最后手段是发射各国的核武器将人类灭亡，对失去“粮食”感到恐慌的阿玛拉只有将小明放了回去。

对速度的喜爱远胜一切的少女琳，作为游星齿轮装置觉醒的她，乘上人鱼姬与大地一决胜负。大地虽然成功地将生命力驾驶舱破坏，但差之毫厘还是让琳成功反应解除。另一方面，一直因为不能对团队做出贡献而感到苦恼的彻平决意代替大地去往宇宙，驾驶着另一部Engine系列机“Nebula Engine”，他漂亮地看穿了琳暴风骤雨般的攻击，并将其成功击退。

六个设计师儿童中的一个人、很伤感。她是爱因上帝公司的研究人员，毬村毛的基础。她毬村是利用自己永远年轻，被需要寻找一种方法。另一方面，伤感的所在查明了和モコ阿马拉，为了确保行动成功，她行动了。研究所碰头的2组发生了枪战。但是先发制人的神秘的资助者“罗宾”的指示毬村的助手、伴kouichi。

The Midsummer's Knights infiltrate an underground ring in search for Baku, the last of the missing Design Children, who is being forced to fight illegal matches for the Yakuza. Amara breaks into the ring and confronts Baku in an attempt to have him remember his past, but is surprised when he refuses. However, neither Amara nor his other companions intend to give up so easily on drawing him back to their side.

Baku refuses to join the other Planetary Gears out of his attachment to Kumiko, the daughter of the local Yakuza. But this changes when the truth about Kumiko comes to surface and Baku decides to take revenge on Earth by helping destroy it.

With no missions to perform in the next days, Daichi and his friends are given a few days of R&R. In the occasion, Hana reveals that she loves Daichi, but fears what he may think of her if she reveals her true self to him. Meanwhile, Amara and Moco take control of a massive asteroid and drop it on Southern Japan with the intention of destroying the Tanegashima Base.

Running away from her friends, Hana meets Setsuna again, and the two end up pursued by Amara and Moco, while Puck, the AI built by Macbeth Enterprises, lays a trap to the CEO and snatches his body. Once Daichi and Hana finally reunite, he reconciles with her, just before the Planetary Gears attack them.

Now finally assembled, the Planetary Gears get the full support of Macbeth Enterprises in their endeavors, unaware of Puck's true intentions. Meanwhile, with Daichi and Teppei still recovering from the last battle, Hana pilots her own machine, the "Flare Engine" to counter another enemy attack.

An inspector from Salty Dog arrives at the Tanegashima Base and questions the merits of the Midsummer's Knights so far. Meanwhile, Moco and Zin launch another attack on Earth, and with Hana's Engine still under repairs, Daichi and Teppei are dispatched to stop them. Salty Dog sends their new remote controlled interceptors to the fight as well, but Daichi and Teppei get themselves in a pinch when Moco takes control of the machines to fight for her.

Daichi, Hana and Teppei board a shuttle to return to Earth, but during reentry, an unexpected change of course leaves them stranded in the middle of Australia. Knowing that they were victims of sabotage, the three battle some enemy forces in the middle of the desert in order to protect Hana from being captured by them.

After hijacking a transport to return home, Daichi and the others are pursued by an unmanned Impacter from Salty Dog, who is determined to capture Hana at all costs for the sake of their plans, but seeing her friends in danger, she takes a drastic measure to save them.

To defeat the Planetary Gears once and for all, the Midsummer's Knights prepare to depart for Uranus in order to destroy the enemy spaceship and render them powerless as part of their master plan, the "Operation Summer". However, Ai, disguised as a model on a PR event, infiltrates the Tenkaido space station to stop them, and the situation gets even more hectic when Salty Dog makes their move as well.

Hana is kidnapped by Salty Dog, but Daichi and the others are too busy dealing with a shower of debris that threaten the space station. When Teppei's impacter is damaged and unable to move, Daichi is forced to choose between sacrificing his friend or allow the Tenkaido to be destroyed.

After averting the previous crisis, Daichi and the others are ready to begin the Operation Summer, but Salty Dog activates their most powerful weapon in order to stop them. Meanwhile, the Planetary Gears succeed to gather enough energy to launch a full scale attack.

On their way to Uranus, Daichi has a strange dream where he meets the Planetary Gears who tempt him to keep living with him in a dream world, but manages to escape thanks to the memories of his friends inside his heart.

At last the Midsummer's Knights reach the Planetary Gears mothership, Auberon. The enemies attempt to halt their advance, but soon after, Puck appears and takes control of Auberon's systems, betraying the Planetary Gears and declaring his intention to take over the entire galaxy.

Puck takes control of Blume while possessing Hana's body and leaves to consume all life on Earth. With the Planetary Gears defeated, Daichi is the only one left on Puck's way, fighting with all his forces to stop it and rescue Hana.