This game seems to take place before The Denpa Men They Came by Wave, judging the fact that Crystal is referred as "childhood friend". The protagonist Denpa Man will once again, request for your help. Instead of going to the antenna tower, you are taken there instantly as the protagonist denpa men will ask you to catch some allies, after doing so, the protagonist will show you a picture of his childhood friend, Crystal, Squelch will be visible behind her as the protagonist later says she's been kidnapped by him. He/she later says to go to Squelch's cave, on the north of the island, if you go to the shop, you will see Mary, Crystal's Mother, saying sorry about asking too much, and she'd go their herself, but she hurt her leg. you'll later find Rick digging in the cave and he gets worried that Crystal's been kidnapped and later begs to join you. Once you get to Squelch and beat him, he says that he handed her over to Sleeky Serpent, when you confront Sleeky Serpent, he says he handed her over to the order and that she will be in big trouble. After going to the order, you will encounter Sleeky Serpent once again. After beating him, you encounter Aflama. Aflama wastes all of your AP as he summons Malignus right after his defeat, beating Malignus will make the fairies come and later seal him, you have now rescued Crystal. There's more! The protagonist Denpa Man will have a nightmare of Best Malignus saying he wants his revenge and you will have to fight him.
Many new antennas has been added the main one being Catch. There is no longer a Denpa Man house, the Denpa Men now house in Digitoll and in residential islands. You don't have to unlock the shop, you get it at the start of the game now. Many new monsters were added. After beating Cave of Darkness 3, you get a boss rematch hall, there is a laser beam in the Antenna tower that lets you stun Denpa Man for a limited time when it's charged up (Unlock using medals) There's a exploration base that you can send 4 Denpa Men to a dungeon to get more money and items. Auto Antenna Tower catches Denpa Man for you (side effects include only when your 3DS is open and it turns off StreetPass. Rental island! Sell useful Denpa Men here! Bazaar island! Sell your items! In the Coliseum, you no longer use battle tickets, you can only play three times per day. In the Antenna tower, Denpa Men can throw paint balls at you if you take too long. When catching, you can hold more in case you catch the wrong Denpa Men.