Phantom and the Knight is a crossover between Danny Phantom and Young Justice, where Danny discovers that he's Bruce Wayne's long lost son, Switched at Birth by a Gotham doctor who was experimenting with nature vs. nurture. If that revelation wasn't earth-shattering enough, circumstances then force Danny to stay with Bruce. Meanwhile, Vlad plots while his wish to keep Amity's ghosts contained and a secret from the rest of the world starts to break down.
- Hero with Bad Publicity: The citizens of Amity Park aren't really fond of the Justice League for ignoring the situation in Amity, not knowing that Vlad's wish is obscuring the ghostly happenings from the outside world.
- Hoist by His Own Petard: Vlad got the Fentons in a contract to head to Peru to investigate ghosts there for two years so he could get guardianship of Danny while they were gone and before the wish keeping eyes off Amity collapses. When he refuses to let them out of the contract when the Switched at Birth scenario comes to light (though admittedly he didn't know why they wanted out at the time), this just ensures that he gets sent to Bruce's for the duration instead.
- Lethal Chef: Maddie wanted to give Bruce a home-cooked meal, but Danny luckily talks her out of it. Later, he mentally notes that eating from ecto-tainted food means that he's not really a picky eater, and being half-ghost has given him a cast-iron stomach.
- The Masquerade: Vlad used a wish from Desiree to keep the ghosts trapped in Amity and keep their existence hidden from most of the outside world, though it's starting to wear off and could disappear any day now.
- OOC Is Serious Business: After visiting Amity and seeing evidence of ghosts firsthand, Bruce realizes how weird it was retroactively that the League unanimously decided to ignore the Amity Park situation as a hoax without even investigating it further, and about how Dick is so quick to dismiss it when Bruce's attempts at sending him footage to analyze comes out garbled. He reacts similarly to realizing just how weird it is that he never questioned why a billionaire like Vlad would become the mayor of Amity.
- Strong Family Resemblance: Danny looks a lot like Bruce. When Vlad meets Bruce while he's in Amity, he recognizes the resemblance subconsciously for the first time due to their similar smiles, but can't place who Bruce reminds him of.
- Switched at Birth: Danny was actually born Isaiah Wayne, son of Bruce Wayne and "Miranda Tate"/Talia al Ghul, Damian's older brother, but was switched with the real Danny Fenton, who died from complications as a newborn, due to a Gotham doctor named van Wagner, who switched hundreds of infants in an unethical experiment on nature vs nurture.
- Weirdness Censor: How Vlad's wish from Desiree works; besides keeping the ghosts that use the Fenton Portal from leaving the city, it also keeps anyone from outside the city from realizing that the ghosts even exist as more than a hoax unless they go to the city and see them with their own eyes, and either destroys photos and video or renders them blurry beyond any hope of usefulness. For example, when Danny gets nervous and accidentally phases his leg through the floor upon entering Wayne Manor, causing him to trip, only Bruce, who's the only Bat-Family member to have seen ghosts by that point, can see that he used his powers, even on the security video, until Zatanna provides them with a charm to allow them to see through it.