In a laboratory which consisted of many scientists working together, such as Professor Oak and Professor Paradox, they were performing research on a newly-recieved Lugia. However, a poison was accidently enjected into the Lugia. However, instead of killing the legendary Pokemon, the poison gave him the ability to speak, an enhanced mind, but also turned him evil and into a shadow version of himself. The Shadow Lugia broke free and flew off. Oak and Paradox agreed to only way to save the world from Shadow Lugia now would be to call together Ash and Ben.
At Bellwood, a bank heist was well on it's way, while in a forest in Pokemon, a trainer was having a battle with Ash. Ben (as Spidermonkey), Gwen, and Kevin eventually stopped the robbers, while Ash's Pikachu managed to beat the trainer's Grotle. At that, a portal opened up and Ash, Dawn, and Brock fell in. Ben's team also noticed the portal opening on a roof, and the kids falling out of it. Ben decided to go check it out and turned into Water Hazard and used water jets to fly up. On the roof, Ash, Dawn, and Brock noticed they were in Bellwood, just as Ben (as Water Hazard of course) came up to them. Ash tried to search for it on the Pokedex, but no matches came up. A now impatient Water Hazard blasted water at them, which leaves Brock to say it must be a water-type. Ash calls Pikachu to use thunderbolt, leaving Water Hazard badly damaged. Ben then turns back from the powerful attack, leaving the three trainers shocked to see it was a human being. Ben goes to turn into Rath, but instead becomes NRG. Pikachu has a tough time beating NRG because of his thick suit, when Gwen comes along and tells Ben that's enough. Instantly, Brock intends to try wooing Gwen. Croagunk was about to use poison jab like usual, but instead, Kevin grabbed Brock by the shirt and threatened him, causing Brock to become terrified. After, Professor Oak and Professor Paradox warped onto the roof as well and explained everything. With that, Ben's and Ash's teams teamed up to stop the Shadow Lugia.
At the Tennyson residence, Sandra was seen in the kitchen, when Jessie, James, and Meowth barge into the room and startle her. They explain Giovanni sent them to find Ben. Sandra doesn't know, so the trio continues looking. Meowth compliments on her cooking, and Jessie and James just grab Meowth and carry him away. Meanwhile, Oak and Paradox explain they need to get to a place that only shows at night to find Shadow Lugia. However, they do not know where to go, so Ben thinks Brainstorm can figure it out. Just as they set off, Team Rocket finds Ben and captures him in a net, then try to get the Ultimatrix off of him, ending up turning Ben into Armodrillo instead. Amadrillo punches the three out of they're balloon and they land infront of the rest of the gang. Ash tells Pikachu to use thunderbolt, which makes Team Rocket blast off. Meanwhile, Brock was staring in awe at a pretty lady, who was actually Charmcaster. Unfortunatley, she, along with Ra'ad and Andreas were attacking them for an odd reason. Ash called out Infernape and Ben transformed into Goop, Gwen and Kevin also attacked. After the fight, Charmcaster, Andres, and Ra'ad retreated, and Gwen wondered why they attacked them. Meanwhile, in a dark, mysterious lair, Shadow Lugia's lair, Charmcaster, Andres, and Ra'ad had told him the whole story, and Shadow Lugia was not impressed and attacked them. The three broke out of the spell and begin to attack Shadow Lugia back, only Shadow Lugia proved to be more powerful. Shadow Lugia told three bird-like figures to get his army ready for a second attack.
The team continued moving through. Before being able to reach Shadow Lugia's lair on Dark Mountain, they had to trek through a forest. It was long before Ash, Ben, and the team got attacked by swarms of Gliscor and Beedrill. Ben becomes Swampfire (even though he really selected Lodestar). Ash called out Buizel, Dawn called out Mamoswine, and Brock called out Sudowoodo. While the fight went on, Giovanni realized that they not only need Ash's Pikachu to get Shadow Lugia, but Ben's Ultimatrix as well. He teams Jessie, James, and Meowth up with Sunder. Back to the fight, Ben has changed to Rath. Ash's Buizel evolves into Floatzel. After defeating them, they find Sunder, Jessie, James, and Meowth and blame them for the attack. Ben becomes Spidermonkey and goes ultimate. Floatzel is easily beaten by Sunder. But after a few minutes of fighting, the heroes won. They continue they're journey.
- Ben Tennyson
- Gwen Tennyson
- Kevin Levin
- Ash Ketchum
- Professor Oak
- Professor Paradox
- Max Tennyson
- Unnamed trainer
- Sandra Tennyson
- Unnamed robbers
- Jessie of Team Rocket
- James of Team Rocket
- Shadow Lugia (originally good; turns back to good at the end)
- Charmcaster (under Shadow Lugia's control)
- Ra'ad (under Shadow Lugia's control)
- Andreas (under Shadow Lugia's control)
- Sunder (hired by Giovanni)
- Pikachu (Ash's)
- Piplup (Dawn's)
- Croagunk (Brock's)
- Meowth (Team Rocket's)
- Articuno (under Shadow Lugia's control)
- Zapdos (under Shadow Lugia's control)
- Moltres (under Shadow Lugia's control)
- Infernape (Ash's)
- Buizel (Ash's; evolves into Floatzel)
- Torterra (Ash's)
- Mamoswine (Dawn's)
- Pachirisu (Dawn's)
- Sudowoodo (Brock's)
- Lugia (becomes Shadow Lugia)
- Grotle (unnamed trainer's)
- Gliscor (multiple; under Shadow Lugia's control)
- Beedrill (multiple; under Shadow Lugia's control)
- Spidermonkey (used twice)
- Water Hazard
- NRG (accidental transformation; selected alien was Rath)
- Armadrillo (activated by Jessie, James, and Meowth)
- Swampfire (accidental transformation; selected alien was Lodestar)
- Ultimate Spidermonkey
- Ultimate Humongousaur
(Water Hazard is hit by the thunderbolt, causing him to turn back)
Ash: It's a person?
Ben: A person with Rath! (Transforms into NRG)
NRG: Or NRG, I guess that's good...
Goop: Sweet moves.
Ash: Thanks. Ben, watch out!
(Ra'ad goes to attack Goop)
Ra'ad: Give in, Tennyson!
- The only time Croagunk appears is when Brock begins to woo Gwen. He is about to use poison jab on him, when Kevin threatens him instead.
- It is unknown how Oak and Paradox know each other.
- The story is similar to the video game, Pokemon XD: Gale of Darkness.
- James makes a Chowder referrence when Sandra calls him and Jessie a couple, he shouts "I'm not her boyfriend!".
- This is the second time Ben uses Ultimate Spidermonkey against Sunder, the first time in The Transmogrification of Eunice.
- At one point in the movie, Rath calls Ash "Ash Ketchup" instead of Ketchum.