We opened in media res with the party investigating a Shinra lab in an office building at 2023 North Fortune Street at 2 am. It was a dead end. As they leave, vigilante Captain Falcon thought they were burglars and accosts them. After this resolves via the use of deputy badges, he gets a signal that a crime is in progress at Light Laboratories and leaves in the Blue Falcon. Roll’s security feed shows a woman breaking into a secure vault, but with stealth technology she can’t identify. The group hustles there, except for Claptrap who goes to run Mission Control for the rest of the session. (Jon was ill.)
At Light Laboratories, Captain Falcon is found unconscious outside the vault. The party enters to see a green gem in the hands of… Samus? She is startled and unarmored, and the police arrive right away. She surrenders without a fight and is arrested. Samus refuses to answer any questions, stating that it wasn’t what it appeared but she cannot give any details. The only two people who were there that night were Guts Man and Cut Man, who are missing that stretch of time in their memories. Lab security footage shows signs of physical memory corruption.
The next morning, the group goes to Police Headquarters. The party cannot speak to Samus because they are not her attorney. Meowth discovers that Pikachu is trying to get into see her as well, but nobody understands him. The duo pull off a Team Rocket Paper-Thin Disguise™, and we learn why that always worked in the anime as nobody in the police station can roll a positive value on their Spot to see that it is two Pokemon wearing a trenchcoat. They go in to speak to Samus, but she will not give much information, stating only that she is very curious as to what that green gem was. Roll, meanwhile, checks Dr. Light’s contact list and finds the defense attorney he would have used had he ever been in legal trouble. Of course, it is Phoenix Wright. Phoenix takes the case because Maya Fey is a Samus fangirl, because that’s how they get most of their cases. Phoenix talks to Samus after exposing Meowth and Pikachu; Meowth remains hidden in the Visitor’s Room as Pikachu rolls the worst Stealth roll ever and attempts to hide under a lampshade. The police chase Pikachu away as Wright convinces Samus to let him represent her; she agrees only on the condition that Meowth (she knows he is listening) and his group provides him constant protection. Being a Phoenix Wright client, she decides not to tell anyone anything useful.
ESCORT MISSION BEGIN! Back at Light Laboratories, Phoenix studies the lab vault. While he does, Cut Man and Guts Man try to attack him! They have purple eyes during this period. The team takes them down quickly, though not without injury. Phoenix finds the following evidence: a blue goo, a perfectly circular warp on the wall of the vault, an equally perfectly circular hole in the roof of the vault, and one of Samus’ rocket heels. Despite being wounded by Cut Man, he manages to escape through the hole in the roof, where the investigation continues.
Phoenix studies the rooftops with only Steve and Maya protecting him… and is sniped. The rest of the party has to rush up there to help because they forgot that this is an escort mission, and once on the roof they must first fight the small legion of Brown Eagles and Giant Bats that fly in to provide cover for the well-hidden sniper. The group deals with the annoying flying enemies, though Revan has to save Meowth from falling off of the roof at one point. After the cover is removed, Phoenix convinces the sniper to surrender. His name is Sniper (Team Fortress 2 strikes again!) and he tells the group that he was hired only a half hour ago, to stand watch and knock off Wright if he started investigating the rooftops of Smash City. The person who did this was a man named Basaquer. Claptrap traces the money to a seedy bar called “Jay’s Bar”. Phoenix finds the following evidence: Strange Indentations, Scorch Marks, and Missile Impact Area.
The trial is about to begin (Initial Trial System!), so the group heads to the courthouse to drop Wright off. Phoenix asks who the prosecutor is, and is told that it is the Chief Prosecutor himself… an intimidating old man who dresses in frilly purple formal clothing. Wright is extremely nervous about this, and arrives at the courthouse to find… it isn’t Manfred Von Karma. No, just some guy named Ganondorf. Revan senses the dark side in Chief Prosecutor Ganondorf more intensely than he has ever sensed in anyone, including the Sith Emperor himself.
The party goes to Jay’s Bar to gather more evidence for Phoenix while the trial goes on. This is the headquarters of a criminal group called the Malice Four. Meowth sneaks in (with help from an invisibility potion) and overhears their conversation; they are coordinating the obfuscation of the investigation on behalf of a woman, and are concerned with someone named Hayabusa. Unfortunately for Meowth, the Malice Four’s gang is comprised of ninja, and one of them manages to spot the fact that there’s an outline of something on the steps. Boss Battle against all four of them (and some mook ninja) commences. Roll takes out the mooks immediately and inflicts heavy damage as the filthy bar drives her berserk, but the Malice Four leader, Bloody Malth, one-shots her. Meowth soon goes down as well, and things look very bad. Steve spots a bomb that the Malice Four member named Bomberhead was constructing, and Revan uses it to force a Mexican standoff. This gets two of the Four (Bomberhead and Basaquer) to retreat, but Barbarian has no fear and Malth believes that retrieving something from a drawer is worth exploding for. The object and drawers are almost destroyed, but Steve escapes with Roll and Meowth’s trophies. Revan blows up the bomb, taking out Barbarian and badly injuring himself and Malth. They battle… and Bloody Malth wins. Through sheer will, Revan untrophies himself… and goes down AGAIN. So he wills himself back again, and finally defeats Malth. Searching the ruins reveals the thing Bloody Malth was so adamant in protecting: an access pad to a hidden control on Samus’ ship.
The group returns to the courthouse with the device JUST as Phoenix needed it to prove that someone else could have used Samus’ ship weapon to disable Guts Man and Cut Man with computer precision and an ion gun, and put the hole in the roof. The party is then asked to go grab her ship entry “blackbox”. When they arrive, they run off the huge dragon Argorok from destroying the ship. They return the blackbox, and Wright wins the trial. Samus uses the evidence posted officially and publicly to publicly reveal the existence and identity of the being known as Dark Samus; Dark Samus would have murdered anyone to keep these things secret, but now they are public and thus special protection is no longer needed. Samus is exonerated, but is very concerned that Dark Samus can now look like HER, and not just her armor. She heads off to hunt down the Malice Four, as the party had no time to detain Malth or Barbarian after the battle.