While Ash and his friends are at the Pokémon Summer Academy, their third lesson is on how to correctly approach Ghost-type Pokémon, when ever and where ever they encounter them. They are then paired up to find a hidden medal in the Summit Ruins. The medal and how fast it's retrieved is needed to get points for the activity. While searching for a partner, Conway has a run-in with a mysterious girl, and is put into a trance. Meanwhile, a boy named Kendall asks to join Dawn, telling her that he'll protect her from Ghost Pokémon. Ash and Angie also pair up, while Brock partners with Mitchell. On the night of the event, the paired-up Trainers head to the Ruins, when a girl is discovered to have been left behind. This alarms Professor Rowan's female assistant who had seen the 10 Blue Team members off moments before.
The Trainers encounter Professor Rowan's tame ghost Pokémon, and handle the situation differently. A Haunter grabs Shinx, and Pikachu attacks it, but Ash apologizes, and they go on their way. Brock, however, gives the Ghost Pokémon some food, and gets safe passage. When Dawn and her partner Kendall come across eating sounds, Kendall fear's he'll be eaten (next) and runs away in fright. Afterward, Dawn sees Conway walking and no partner. She goes to investigate just as Conway is coaxed towards a cliff by the ghostly girl. Conway is about to walk off a cliff when Dusknoir grabs his arm, waking Conway from his daze. Though safe, Conway faints at Dusknoir's appearance. Dawn stumbles upon Conway on the ground, with Dusknoir ominously overhead. Dawn misinterprets the scene as Dusknoir has hurt Conway, and she confronts it yelling, "Alright, what did you do to Conway?!" The Dusknoir exclaims and waves its arms before fading away. Dawn rushes up and wakes Conway. Conway explains to Dawn that he was following a girl, and according to what the Pokédex said about Dusknoir, Dawn and Conway incorrectly assume that Dusknoir took the ghostly girl to the spirit world, and was about to take Conway too.
Meanwhile, Meowth attempts to scare Ash and Angie, but incapacitates himself after literally zipping his lips in a Banette disguise's zipper mouth. Missing his opportunity, Meowth continues to attempt to unzip his lips, when a real Banette helps him. Thanking the Banette, Meowth realizes he's surrounded by Ghost Pokémon, scaring Meowth off. After he reaches safety, Meowth is lured by the girl with food, but is stopped by Dusknoir. Meowth starts yelling, but then gets scared when he realizes it's a Dusknoir. Like Conway, Meowth is scared into fainting, and discovered by Jessie. Jessie is then confronted by Dusknoir. Jessie freaks out and drops Meowth, then runs away leaving Meowth and her partner behind. Jessie runs past Brock and Mitchell, with her partner behind her carrying Meowth. Brock and Mitchell wonder what had scared them away, but then they too are approached by Dusknoir. Brock tries offering some food to the Dusknoir, but the Dusknoir rejects the food and uses Will-O-Wisp at them. After Brock and Mitchell run away, Dusknoir spots the ghost girl in the bushes nearby.
Jessie and the others run back to the Academy, and report about the Dusknoir, as Ash and Angie meet a Misdreavus. Misdreavus uses Screech, and makes Ash and Angie run away and get lost. The girl appears and then beckons Ash and Angie to follow her, while the others have made it back to Professor Rowan. Being that Pokémon in the area are monitored and documented, the reports of a Dusknoir is alarming to Professor Rowan, especially since Dusknoir is a forest-dwelling Pokémon with no need to be in the area. Rowan also explains that an accident occurred one day when a mysterious cave was uncovered behind a wall. He also states that it might be the entrance to the spirit world, and that he assumes Dusknoir is trying to take someone there. Conway tells Rowan that he followed a girl and he thinks Dusknoir has taken her away.
It is concluded by Professor Rowan that the Dusknoir must have originated from a mysterious cave, which is thought to lead to the spirit world. Meanwhile, Ash and Angie finally get to the Summit Ruins, and get the medal first. There, the girl tries to coax Ash and Angie into the cave Professor Rowan mentioned, when Dusknoir appears. Dusknoir prepares to attack the girl, but Ash and Angie battle Dusknoir to protect themselves and the girl. Pikachu and Shinx attack while Dusknoir's back is turned on them. Dusknoir is momentarily stunned, and the girl tries to suck them into the spirit world through the cave. Angie is pulled into the air, but caught by Ash who holds onto her. Meanwhile, everyone arrives at the spot, and Professor Rowan prevents anyone else from getting too close. Dusknoir gets up and grabs Ash and Angie, then sticks its tail into the ground to keep from getting sucked into the portal. Ash and Angie are shocked and realize Dusknoir was trying to protect them all along.
After a few moments, the portal starts to drag them closer, with Dusknoir's tail moving through the dirt. Ash and Angie freak out, and Dusknoir turns around and blasts the girl, collapsing the cave entrance. After everyone thanks the Dusknoir, the Dusknoir flies off and disappears. It turns out that the girl was a ghost and Dusknoir was trying to stop her. Conway panics at the fact that he was partnered with a ghost the whole time. The next day Professor Rowan awards each team 30 points for a job well done. None of the teams gained an advantage, and the Blue Team leads by 260 to the Red Team's 220. Ash isn't discouraged as he rallied for the Red Team to turn the tables and take the lead as the episode ends.
- The title is a pun of the phrase "school days".
- The dub title of this episode is similar to Sick Daze and Training Daze.
- An updated version of the music from the Sealed Chamber, Desert Ruins, Island Cave and Ancient Tomb in Ruby, Sapphire, and Emerald is used.
- Ghost types introduced in each of the four generations appeared in this episode.
- Similar to the previous episode, this episode also features scenes of hypnotic trance.
- In one scene, Ash mentioned to Pikachu to just count to ten when a Haunter grabbed Shinx's tail and Pikachu zapped it. This could refer to a Japanese myth about a ghost who is unable to count to ten, then suddenly disappears. It could also refer to the common teaching in America to control anger.
- Like Darkrai, who was framed for things it didn't do, Dusknoir finds itself in a similar situation. Even music from The Rise of Darkrai is used in Dusknoir's scenes. It's also worth mentioning that both Darkrai and Dusknoir are main antagonists in Pokémon Mystery Dungeon: Explorers of Time and Explorers of Darkness, and they are final boss Pokémon in Pokémon Ranger: Shadows of Almia's main storyline as well.
- The book Pokémon Academy is based on this episode.
- In one scene, Professor Rowan's neck and ear are the same color as his hair.
- Dango is called a fried cakeball skewer.