Tomoki Sakurai's peaceful life is now long in the past, because he has to deal with two angeloids, Ikaros and Nymph, as well as with his friends from school, all of whom are very special in their own ways. Tomoki's recurring dream about an angel warning him from the rage of heavens is becoming very common, until one day a new angel, who is as powerful as Ikaros, arrives Earth with the sole purpose of terminating Tomoki—his dream is starting to connect both realities, the Earth and the Synapses.
Tomoki has another dream where the mysterious angel warns him of another Angeloid and after revealing the information to his friends, Nymph suggests they visit his dream via Dive Game which enables them to visit humans' dreams. The group, consisting of Tomoki, Sugata, Mikako and Suhara, leave into the dream to find themselves confronted with each other's dreams and an embarrassing revelation for Suhara. Ultimately, they are unable to visit Tomoki's dream and instead land on a bizarre world with a pillar with illegible words and hibernating evergreen trees. They return with more questions than answers and Sugata finally remembers a forgotten memory a year past when Ikaros first fell onto the Earth and winesses Astraea's arrival.
Tomoki, much to his irritation and confusion, finds himself aroused by the antics of Ikaros and Nymph. This disturbs him greatly so he leaves for the mountains to train in the Zen monastery. At the same time, Astraea, the new angeloid lands at the monastery to dispatch Tomoki while Sugata informs the rest about her. Nymph and Ikaros ignore the threat calling Astaea an 'idiot' and leave Tomoki alone who himself is finding trouble ridding himself of his 'earthly desires'. Later, Sugata discovers Astraea and learns of the threat to Tomoki's life and more information on Synapse, the world where Angeloids come from.
After unexpectedly divulging information of her assignment, Astraea attempts to attack Sugata to keep her secret safe. Unfortunately, she falls into the hands of Mikako, who upon seeing the gullible nature of the new Angeloid, fools her into joining a wrestling match at the local festival. Much like last time, Mikako entices Tomoki to join by putting up a prize of ten million yen and a chance to bathe with her family's geisha. Nymph wrestles with her emotions after losing her wings and master and finds herself yearning for a new one, Tomoki being her new candidate.
Winter comes to the city and Astraea is still far from completing her mission of eliminating Tomoki. Mikako reels her into another of her sadistic tantrums and stages a mock battle between the girls and boys of her school by appointing Tomoki as the general of the boys' group while acting as the general of the girls' group herself. This time, she entices Tomoki to fall into her trap by putting up the reward to be able to do anything to the losing team. Nymph still yearns for a new master and Astraea faces a dilemma when she is unable to dispatch Tomoki due to his question to her actions being her own choice or not.
Sugata and Sohara travel to Synapse with the aid of Nymph. Sohara accidentally drops an object onto the world below which falls into the hands of Tomoki who fashions it into a pedal bike that transforms into a robot. At Synapse, the two humans learn new details about the New World while Tomoki relishes his time with his new toy to satisfy his perverse actions. Sohara later destroys the toy and a new Angeloid is revealed post credits.
Astraea gets enrolled at Tomoki's school and tries unsuccessfully to dispatch of him. Later on, Nymph, Mikako, Sohara, Tomoki and Astraea join in a quiz competition to determine that Tomoki himself is not an 'idiot' as labeled by his schoolmates. His attempt proves futile and the events leave him to be an 'idiot' to the whole city than just in the school before. Astraea finds herself spending time with the group and acceptance which adds onto her dilemma and Daedalus discovers that Chaos, the new second generation Angeloid has been sent to Earth.
Tomoki has a dream where Daedalus warns him of another Angeloid who then interrupts the communication and chokes Ikaros. While Ikaros shops for groceries. Nymph is pulled away for a date by Tomoki.
Ikaros arrives to assist Nymph against Chaos. Daedalus reveals to Sugata that she is the creator of the First generation Angeloids which include Ikaros, Nymph, and Astraea. The time has come for Astraea to make a choice: will she do the Sky Master's bidding and destroy Ikaros and Nymph once and for all, or will she listen to Tomoki and find the strength to choose her own destiny? Astraea chooses the latter, and fights Chaos using her Aegis shield and sword, but Chaos is still able to get the upper hand. Ikaros arrives and fights Chaos, eventually plunging her to the depths of the sea so that she passes out.
For this year's Satsukitane Festival, Mikako holds a Yo-Yo Fishing contest where all the girls, except Ikaros and herself, are tied up in a pool, and the guys tied on ropes must grab them out of the water.
Tomoki seeks some alone time from the girls, first in the bathroom, until he is washed out, and then in a closet where he is almost cooked and then washed out again. Astraea and Nymph each visit but Tomoki chases them out. Sohara visits but instead of giving him a karate chop, she asks why he still peeps despite having beautiful Angeloids in his house, and why he does not harass Ikaros.
With Ikaros feeling ill, Sohara and Tomoki go to school where Sugata and Mikako are watching the typhoon. Later, Astraea investigates a twister, but is attacked by Chaos, while Ikaros continues to struggle with losing her memories. Tomoki goes through the Dive Game portal to meet Daedalus, who gives him a lock, while Nymph and Ikaros join Astraea against Chaos. The Angeloids retreat and plan a coordinated attack but it fails. Tomoki returns and tells the Angeloids to live, and that he will be the master for Nymph and Astraea. The Angeloids manage to free themselves and are revitalized by his love. Nymph generates new wings, and uses a hacking field to boost Astraea's and Ikaros's combat powers. After Ikaros launches her attacks, Astraea does one final lunge, knocking Chaos to the ground. Despite Chaos's pleading to be loved (killed), Tomoki arrives and pets her head, and Chaos starts to experience feelings of genuine love. Tomoki then puts Daedalus's lock on the collar chain of Chaos.
Chaos is returned to Daedalus. Things return to normal, with Nymph restoring Ikaros's memories, and Ikaros learning bathroom etiquette, but Tomoki has one more perverted task: transforming into pool water so he can fondle girls during swim class.