The story begins when Matagu Shido one night accidentally dials to Earth's Assistance Hotline, and his call is answered by Peorth. After the initial shock, Peorth explains to Matagu she's going to grant him a wish, anything he wants. Discarding his original wish to meet an alien or an otherworldly being, after some thought he decides to wish for a date with his teacher Mizuho.
However, when Peorth is in the midst of approving Matagu's wish, the demoness Mara senses her presence and decides to have fun sabotaging her, and cuts her connection to Yggdrasil, rendering Peorth powerless and unable to return to heaven or call for help. Understanding that she's in trouble, Matagu offers to take Peorth somewhere she can contact her friends to solve this issue, but since he doesn't have a car to get there, he'll have to ask his teacher who lives nearby.
Meanwhile, in two different locations, Kei Kusanagi and Keiichi Morisato are about to see their respective wives, only to find themselves each a woman they've never met before, but who insists they've been together for a long time. Somehow, Mara's meddling has caused Belldandy and Mizuho to switch places with each other too! It seems that things almost never go as they're supposed to, especially around goddesses, demons, and half-aliens.
Onegai Megami-Sama! provides trope examples of:
- Adaptation Personality Change: Zigzagged with Matagu. He keeps his personality from the original series, rather than turning into his BrotherSister Incest-obsessed self from the sequel.
- Alone Among the Couples: Koishi feels this way when she notices that almost everybody around her is pairing off: Hyosuke and Kaede, Keiichi and Belldandy, and much to her shock, Mizuho and Kei.
- Alternate Universe Fic: The story picks up shortly after the OVA episode of Please Teacher!, thus ignoring the events of Please Twins!.
- Because You Were Nice to Me: Happens both ways with Matagu and Peorth. Matagu falls for Peorth after she makes him feel special when no other girl ever did, while he endears himself to her by helping her when she's in trouble rather than taking advantage of her.
- Brought Down to Normal: With her connection to Yggdrasil severed, Peorth is unable to use her powers and is left as vulnerable as any mortal. Fortunately, Matagu is a kindhearted young man who refuses to take advantage of her in that state, and does everything he can to help her.
- Cool Bike: Agent #42 has one. Skuld appropiates it when he leaves it behind during his escape.
- Damsel in Distress: Mizuho and Peorth become this during the third act, when they're abducted by Agent #42. Fortunately, Kei and Matagu are able to rescue them before they leave the Sol system.
- Did You Just Punch Out Cthulhu?: Agent #42's weapon packs enough power to knock out a goddess, as shown when she uses it on Peorth. Only for a short while, though.
- Don't Ask: Kei answers this to Matagu asking him how he knows where Mizuho keeps her car. Given everything that has happened up to that point, he decides it's better that way for the time being.
- Fish out of Water: Agent #42 has a... tough time blending in with Earth's customs.
- "Freaky Friday" Flip: A variation. Belldandy and Mizuho retain their bodies and personalities, but end up switching places and memories about their lives, so they believe they're married to Kei and Keiichi respectively instead of the other way around.
- From a Certain Point of View: When Mizuho and Kei have to come clean about their marriage to Kei's friends, most of what they say is true, including the fact that Mizuho cared for Kei when he fell into one of his "standstills". Of course, Mizuho doesn't bother to correct them about Kei entering the love hotel with her mother instead of herself.
- Gratuitous French: Peorth often uses French words in her speech.
- I Just Want to Be Loved: Koishi confesses this to Belldandy after she gets heartbroken when she finds Kei and Mizuho making out.
- Insecure Love Interest: Matagu struggles with this at the beginning, wondering if Peorth would really like him for him, especially after he finds out she acted the same way to Keiichi when they first met.
- Internal Reveal: When Peorth finds Belldandy at Mizuho's house, and later when they find Mizuho in the Tariki-Hongan temple, they're forced to become clean about their real statuses as goddesses (and alien in Mizuho's case) to solve the trouble much faster. Matagu also learns of Kei's marriage to Mizuho.
- Lap Pillow: Matagu ends up resting on Peorth's lap, when he faints after meeting her.
- Love Hurts: Koishi has to learn this the hard way when she finds out Mizuho and Kei are married. Mizuho explains to her that marriage isn't all happiness, but also fighting and sadness every once in a while.
- Magical Girlfriend: Aside from the canon examples of Belldandy for Keiichi and Mizuho for Kei, Peorth becomes this to Matagu.
- No Name Given: We never find Agent #42's real name.
- Not Distracted by the Sexy: Agent #42 mentally acknowledges Peorth's beauty when he sees her, but that doesn't stop him from shooting her with his weapon to leave her out cold and abduct her.
- Shipper on Deck: Matagu's family, especially his sister Haruko, are very approving of his relationship with Peorth.
- The Tease: Peorth is this as per canon. Matagu is worried that she's like this to everyone, but once they get together, she quickly directs her teasing to him, and only him.
- Tempting Fate: Happens in a positive way. Matagu muses that there's no way a girl was going to fall from the sky for him, right before he meets Peorth.
- You Sound Familiar: In-Universe, people notice that Mizuho and Belldandy have similar voices, to the point Kei and Keiichi briefly mistake them for the other when the "Freaky Friday" Flip happens. Obviously this is a reference to both of them being voiced by Kikuko Inoue.