Tazuna is a young boy who loves to fix things. But his life takes an unexpected turn when he meets a girl who's lying on a hospital bed in an electronically locked lab. When he takes her hand, he finds out that he can never let go, or she will die. On top of that, he has to battle a man and his partner in something called the Ziggurat, and he doesn't have a power of his own. Can he unlock the might of the Hand Shakers?

Tazuna and his new friend Koyori have a problem: If Tazuna lets go of Koyori's hand, she'll die! Can he take her home with him and explain to his parents why he now has to live with a girl? And how's he going to take a bath with her!?

Tazuna meets Chizuru and Hayate, the pair who's car he fixed on the day he met Koyori. They're workers for a major food corporation in the area, and they offer to treat him and Koyori to dinner as a thank you. But after the meal, they reveal that they're actually Hand Shakers themselves!

After the battle inside the Ziggurat, Chizuru and Hayate are horrified to find out that their victory would have cost Koyori her life. They agree to help Tazuna and Koyori, even though they're out of the fight now. They tell the two of them that in order not to be found in the real world, they need to come up with a name to use inside the Ziggurat when they fight. After a bit of thought, Tazuna and Koyori's new name becomes "Single Gear".

Koyori gets separated from Tazuna, and because she doesn't have a cellphone, she doesn't have a way to get in touch with him. Fortunately, she's found by President Lily and her little brother Masaru, who take her to play the new game, Precious Memories. Koyori shows an amazing talent for the game, but things take a sudden turn when Lily and Masaru are revealed to be Hand Shakers as well.

Lily and Masaru insist on fighting Single Gear, despite Tazuna's fervent protests. The two of them use cards: Lily, her Tarots, and Masaru, his precious memories deck. But because Masaru is using the same strategy he does in the game, Koyori knows how to beat him. Can she share this with Tazuna when she isn't able to speak?

It's time for the School Festival, and Tazuna's class is in big trouble! The machinery's broken and the cooks broke their arm, and they've got no way to get the cheap ingredients they need for their food stall. Can Tazuna use the connections he's made so far to make everything right? And can Koyori learn to cook in time?

Tazuna and Koyori meet their next opponent: Kodama, a powerful idol singer who has defeated many other Hand Shakers. She and her producer are their toughest opponent yet, and together, they overwhelm Single Gear. Tazuna barely escapes into the water below a nearby bridge...

Tazuna and Koyori battle Awaza Kodama a second time, and she's just as powerful as the first. Tazuna, and Single Gear, cannot hope to defeat her. Their only choice is to rely on Koyori's unseen strength.

With the last of their foes vanquished, and Koyori now having the ability to talk, it's time for her and Tazuna to take up a part time job at the local Cocktail Corn. It's a time to reflect on what's gone on so far, meet old friends, and ready the pair for the future.

Makihara once had a partner, and a boss. Together they researched the Ziggurat, and the mystery of Babel's revelations. But when a pair of Hand Shaker children were born, their lives changed. The children were constantly targeted, and if they were defeated, they would die. Makihara and his partner tried their best to defend the children, but years of fighting wore them down, and they had a falling out. Now his partner is back, and he has a demand: put Koyori back to sleep forever, and separate her from Tazuna.

Tazuna and Koyori are facing off against Koyori's sister and the doc's old partner. Koyori's sister has been reduced to an emotionless mute after years of difficult treatments and abuse. Can the two of them bear to hurt someone so close to Koyori? And even if so, can they win against Handshakers who are so much more powerful and determined?