The movie picks up three years after Freddy vs Ghostbusters and after Ghostbusters The Denver Chronicles (Web Comic). Ed is the host of his own science show, Science of the Universe, Eugene has been replaced as the third team member by Pavel Karnov.
Reporter April Hunter is assigned to do a story on the Denver Ghostbusters because of their popularity, even though she considers the story beneath her. April expresses more interest in a story on Egyptian artifacts at a local museum. Her boss allows her to follow up on that story if she does the story on the Ghostbusters, and April reluctantly accepts. Neil Anderson initially blows off April's request for an interview, but after realizing who it is (he considers the reporter a "hot chick") he changes his mind. He fails to impress her during an interview by setting the ceiling on fire with a proton pack and overloading the containment unit so Ed has to rush over from taping his show and fix it.
That night Ed’s worried by a news report on Dr. Klaus Constantin, a wheelchair bound archeologist, and the major Egyptian artifact from the story April wanted to cover: the Amulet of Anubis. Supposedly it can be used to open portals to the afterlife. Constantin had been secretly researching the amulet to turn the results over to a weapons developer, but when they cut off his funding he steals it and plans to use its powers for himself. He tries to invoke its power with an arcane ritual, but realizes it won’t work unless it’s energized with human souls. Constantin sneaks into Ghostbusters HQ, chloroforms the secretary and steals a trap which he immediately uses to steal the soul of a homeless man he runs into behind the building. He performs the ritual again and succeeds in activating the amulet, and rises from his wheelchair.
Things start to go south for the Ghostbusters. Ed’s canned from the show and replaced by Levar Gordon, a “jive” black man, in hopes of drawing more interest from young viewers. April’s told by her boss to do a weeklong follow-up on her Ghostbusters story, but having met them she’s reluctant to make them look foolish. At a bust at a movie theater, Neil badgers Ed into letting him try out the Neutrino Pack, a new model of the proton pack, but untested and unstable. In the course of the bust he hits the ghost with such a powerful beam it’s completely destroyed, leading Ed to ream him for his irresponsibility. Their reputation is smeared even further when Constantin steals the souls of the theater’s staff, making it seem as if the Ghostbusters are responsible. Levar is one of many locals protesting them, and the authorities impound most of their equipment.
Neil makes the best of things and scores a date with April (but is ribbed by her super for not going for the kiss). Constantin is waiting in her apartment and offers to make her his queen when he takes over the world with the amulet’s powers, but leaves when the super enters after hearing raised voices.
April swings by Ghostbuster HQ to talk over breakfast, and Ed discusses his theory that a ghost trap could be the cause of the soul thefts. He explains Dr. Stantz's theory is eyes are windows into the soul and by looking directly into a ghost trap the soul can be drawn out (elaborating on Ray’s warning not to look into the trap from the first movie). Ed asks Pavel about Constantin’s character to see if he could be reponsible, as Pavel used to be his student, which infuriates Neil for feeling like the others don’t trust him enough to keep him in the loop. He storms out.
Constantin has gathered enough power to open portals using the amulet, and an outbreak of ghosts grips Denver. City officials desperately rearm Ed and Pavel and send them to stop the cataclysm. They confront Constantin but he summons an enormous ghost dragon. Ed and Levar team up to battle it in the streets in the Ghostbusters’ van, and they destroy it after a protracted chase. They return and recover the stolen souls with several traps mounted together, but a demonic being begins to crawl out of the portal and their proton packs prove insufficient to drive it back until Neil shows up in the Nick of time and blasts the demon back through the portal, with Constantin close behind, with the Neutrino Pack. The pack starts to overload but they throw it through the portal, destroying both it and Constantin. The Ghostbusters, exhausted from saving the world, turn down an interview to get some well-earned rest.
- Notably, a reference to the film is made in Ghostbusters: The Video Game. During free-roam of the firehouse between missions, a crayon drawing of "Uncle Egon" by "Ed" can be found in the basement. As the video game is considered canon, that means that Return is also canon to the series.
- Ed's ringtone is the Legend of Zelda overworld theme.
- During the Ghostbusters' battle with the ghost dragon, one of the people watching is the Angry Video Game Nerd.
- Pavel Karnov's name is a reference to Star Trek's Pavel Chekov and to the videogame Karnov.
- LeVar Gordon's name is a reference to LeVar Burton (the actor who played Geordi LaForge in Star Trek: The Next Generation.
- April Hunter is a journalist and her name is a reference to April O'Neil, the journalist of Teenage Mutant Ninja Turtles.
- When Neil and Pavel are at the bar, the song playing in the background is Tarzan Boy by Baltimora, which also played in the bar scene in Teenage Mutant Ninja Turtles III.
- The motion detector looks like the one used in Aliens.
- The amulet of Anubis looks like the Amulet of Ra in Raiders of the Lost Ark.
- The agents who take the Ghostbusters' equipment away are referred to as Agent J and Agent K, like the main characters of Men In Black.
- The agents and the secretary discuss about Batman and Robin.
- When April's boss interrupts all feeds to broadcast the live coverage of the battle with Constantin, a music video is briefly shown before being cut off. It's Cyndi Lauper singing "Goonies R Good Enough."
- The supernatural tornado that erupts from Klaus Constantin's apartment is referred to as a "soulnado", a term that was first used in Mortal Kombat games.
- The "ghost dragon thing" is said to resemble Falkor, the dragon character in The Neverending Story.
- The Neutrino Pack has a neutrona wand that attaches to the Ghostbuster's arm rather than mounted in a handheld gun. This is close to the original design for the Proton Pack.
- As a throwback to the previous film, Freddy Krueger's trademark sweater and claw glove can be seen next to the containment unit.