Phineas and Ferb find a mysterious capsule, while Dr. Doofenshmirtz goes missing.
- Alternate Universe: The episode is revealed to take place in one, as indicated by the number of stripes on Phineas' shirt. And his dad being a polar bear. On a more subtle level, Ferb is far more talkative in this episode than usual.
- Call-Back: Unfortunately, Buford can't hold on much longer to the tree branch since his TUFF SHOO LAYSIZZ!!!!!! are being washed.
- Chorus Girls: As always, Doof's song is accompanied by this, baffling Professor Mystery.Professor Mystery: How did you get chorus girls in here?Doofenshmirtz: Ah, they're union, they'll travel.
- Connected All Along: It's revealed near the end of the episode that Bernie and Denise are Prof. Mystery's parents.
- Deconstructed Character Archetype: Professor Mystery merrily takes apart the Hidden Agenda Villain and No-Nonsense Nemesis. He repeatedly insists that "mystery is his allure" and refuses to disclose information regarding his plans, devices or backstory, thus forcing his nemesis Peter the Panda to focus entirely on thwarting his evil schemes. Instead of making him intriguing, this attitude makes him look pathetic and pretty boring. Doofenshmirtz cannot take him seriously or feel threatened by his "true-purpose-shrouded-in-mystery-inator" since he has no idea what he's trying to do, and his relationship with Peter has suffered the equivalent of a communication breakdown because Mystery's lack of gloating means he and Peter never gain much of a rapport, leading Peter to cheat on him by thwarting Doofenshmirtz.
- Does This Remind You of Anything?: Continuing the trend in Peter the Panda episodes, a nemesis-relationship is treated like a romantic relationship. In this case, Doofenshmirtz is treated like a homewrecker who interfered with Peter's relationship with his nemesis. Doofenshmirtz didn't even know Peter had a nemesis, and claims he wouldn't have fought Peter otherwise if he knew he was just "the other evil scientist." Doof tries to get Professor Mystery to communicate more with Peter so Peter will be more inclined to stay with him.
- Doof also calls Peter "more of a thwarty call" than a nemesis, an obvious pun on "booty call."
- Mystery demands to know what Doof gave Peter that he couldn't. Heinz assumes an evil monologue.
- Failure Is the Only Option: The kids exploit this happening to Candace. After the black hole in Bernie's capsule breaks it's containment, Baljeet bemoans the fact something in the backyard hasn't disappeared, Buford bemoaning this seeming break in the pattern. Isabella points out that it's not actually a break in the pattern, interrupting herself as the realization sinks in for everyone that Candace hasn't tried to bust them yet. They all cry out for Candace in order to get her attention, knowing the capsule and the black hole will disappear before she shows Linda.
- Gainax Ending: The last scene reveals the events of the episode were really an Alternate Universe viewed through a portal made from Phineas and Ferb's sorbet machine.
- Green-Eyed Monster: Professor Mystery finding out that Peter the Panda sometimes thwarts Doof leads to him kidnapping Doof out of jealousy and planning to eliminate him.
- I Want You to Meet an Old Friend of Mine: Rob Morrow and Jane Kaczmarek, who play Bernie and Denise, previously worked together on Jenifer.
- Malevolent Masked Man: Professor Mystery wears a ski mask at all times.
- Poor Communication Kills: Doof figures out that this is problem in Peter and Mystery's relationship: Peter can't talk and emotes way less than Perry, and Mystery doesn't pick up the slack with monologues, backstories, or explaining his inventions in any way.Doof: But he's your nemesis! He's got to know what he's thwarting; that's just common courtesy!
- Running Gag:
- Bernie keeps claiming he's one of the kids from the future.
- Professor Mystery insisting "Mystery is my allure!"
- Sherlock Scan: Perry, upon entering Doof's ransacked lair, analyzes small things like footprints and Doofenshmirtz's abandoned computer to figure out Doof was kidnapped. He becomes more worried with every deduction.
- Whole-Plot Reference: This episode acts as a tribute to Lost. Co-creator Damon Lindelof is credited with the story, as he suggested an episode revealing Peter the Panda's actual nemesis. Also, Terry O'Quinn, who played Locke on the series, voices Professor Mystery.
