The story commences with a rock band by the name of Trip Cyclone that stops in the small town of Cyclone, Arizona while scouting out locations for music videos. The town seems to have gotten stuck in time decades ago, people are strange and not welcoming to outsiders. When two hikers disappear in the wake an ancient Indian curse, members of the town set out for a search expedition, only to lose one of them in the process. The town's population slowly begins to dwindle, tourists stop coming in, and the only way out of Cyclone is blocked by a rockslide, trapping the band. Things only get worse when they are approached by a strange man wearing a traditional Indian Kachina mask, who calls himself Darkcloud. As a personal friend of the band, you are tasked with finding ancient prayer sticks called "Bahos" in order to lift the curse from the town and also figuring out where Trip Cyclone and the rest of the town have disappeared to.
Like the original Shivers, Shivers Two is heavy on puzzle gameplay ranging from Enter Solution Here to Guide Dang It!. The "flashback" feature also returns, where the game stores any code or a solution to a puzzle you come across as a "memory" to help avoid backtracking and note taking. In addition to this, Shivers Two adds instant teleportation to any area you've been to before. A key difference occurs in the method of sealing the evil. Where Shivers made it fairly easy to avoid taking anything but scripted damage, Shivers Two is not so kind because the sealing occurs during a Death Course. You want to survive? You better be quick.
Shivers Two: Harvest of Souls has examples of:
- Abandoned Area: The town of Cyclone. Once a quaint little town, it isn't until Trip Cyclone's arrival that things begin to change. Townsfolk are disappearing left and right, those who remain begin quarreling with each other, and they begin to blame the band for the disappearances. Too bad they don't realize the town was built on an ancient burial ground.
- Always Night: Justified, as the whole game takes place in one night.
- Apocalyptic Log: You can find a journal from one of the band members detailing their first impressions of the town to their meetup with Darkcloud and the disappearing townsfolk. Various answering machines can also be found scattered around town which reveals the various quarrels the townsfolk have regarding the events that are unfolding.
- The Cameo: The corrupt sheriff in the sequel is visually portrayed by Al Lowe.
- Curiosity Killed the Cast: By the time you arrive, only two people are left, the motel owner and Max. Everyone else has been turned into petroglyphs.
- Death Course: As soon as you pick up a Bahos, it starts draining your life force. To stop it from doing that, you have to go to Devil's Mouth Canyon and use it on one of the many petroglyphs there. The only way to know which petroglyph is the right one is to pay attention to the area you pick up the Bahos in, because an image of it will be around. So the most efficient course of action is to go to Devil's Mouth Canyon before picking up the first Bahos so that it becomes a teleportation option from the get-go and then to inspect a room thoroughly before bothering with the Bahos.
- Enter Solution Here: As with its predecessor, quite a few puzzles involve hints from around the town.
- Fake Band: Trip Cyclone, complete with full versions of their songs from the game's soundtrack as CD-Audio tracks.
- Ghostly Goals: Type A shows up: Norah Wharton, Darkcloud's murdered wife. He wants to avenge her, she disagrees with killing and/or cursing people.
- Hearing Voices: Many tracks in the game use various vocal tracks from the five Trip Cyclone songs featured on the second disk that doubles as an audio CD. This is evident in the church, which is simply the backing vocals to the song "Spell it Out".
- I Don't Like the Sound of That Place: "Devil's Mouth Canyon" certainly has an intimidating ring to it.
- Last-Second Ending Choice: There are three endings and which one you get depends on a choice so late that with one exception it'll be your last action in the game. Trust either of the two and you get the bad and mediocre endings; do it right by doing it yourself and you have to solve one last puzzle. Failing to solve the puzzle leads to a gameover.
- Mass Hypnosis: If you watch TV without taking precautions, you will be hypnotized and reawaken in Devil's Mouth Canyon. This is how so many of Cyclone have disappeared. The only way to stop this from happening and get access to the clues on TV is to block off the red light next to the screen with gum.
- Maligned Mixed Marriage: A central part of the background story. The townspeople aren't happy about Norah marrying the outsider Max Wharton and when she dies due to their carelessness they look forward to making Max's life hell now that she's out of the way.
- Mythology Gag
- You can find one of Windlenot's books in Cyclone's library.
- One of the Trip Cyclone members can be seen wearing a Shivers shirt.
- Point-and-Click Map: The in-game map allows you to instantly visit any place you've already been to once before. This is especially useful to cut down on the time you have a Bahos with you.
- Police are Useless: After the disappearances of the locals become more common, the sheriff doesn't even bother with filling out missing-person forms. He also doesn't do anything about the landslide that blocks the only exit from the town, something the general store and gas station owner Phil doesn't like as the lack of new inventory is hurting his business.
- Portrait Painting Peephole: There's one in the library to spy on the conference room. While you're inside, you can walk up to the painting to see another's eyes dart around before settling on you without so much as blinking. By the time you're at the door to apprehend your stalker, he's already gone.