The Bakugan anime is nothing to write home about. The story is a fantasy-oriented version of Digimon; a group of young children befriends creatures from another world. Together, these friends have to work together to save both of their worlds. Thrown in were elements from Pokémon (the elemental typing of the monsters and the emphasis on tournament-style battles) and Yu-Gi-Oh (the role that cards play in said battles).
In short, the series wasn't breaking any new ground. As for the dub... anime fans didn't know what they were missing with 4Kids Entertainment. That's not to say the series was a total wash. One of the brighter elements was a twist surrounding Season 1's villain, Masquerade—he turned out to be an alternate identity of the hero Alice. This was a well-laid twist that furthered both characters; Alice is forced to confront that she was unknowingly working against her friends the whole series, but learns to use her alter ego to help them.
9 Alice & Masquerade Never Appear Onscreen Together
One of those hints that only becomes obvious once the viewer knows the twist; unlike the other Battle Brawlers, Alice never appears onscreen with Masquerade. In Masquerade's introductory episode, "Masquerade Ball," both Runo and Dan come face-to-face with him.
In episode 13, "Just For The Shun Of It," Masquerade tries (and fails) to recruit Shun to his cause, but not before they battle Dan together. Julie and Marucho come face-to-face with him when Dan and Masquerade battle in Episode 27. Never Alice, though, because she and Masquerade are one and the same.
8 The Battle Brawlers Don't Have A Darkus Member... Or Do They?
There are six Bakugan types: Pyros (Fire), Haos (Light), Aquos (Water), Ventus (Air), Subterra (Earth), and Darkus (Dark). The Battle Brawlers have six members, one for each type... except Alice, who doesn't brawl. Masquerade is instead the primary Darkus brawler in the series.
At first glance, this makes some sense; Darkus is framed as the "evil" element, so naturally, the villain is the one who wields it. However, when Alice accepts Masquerade as a part of her, she takes over as the Darkus Brawler on the team, using Masquerade's Darkus Bakugan as her own.
7 Masquerade Is The #1 Bakugan Brawler, Alice Is The #1 Bakugan Strategist
Alice is the one member of the Bakugan Battle Brawlers who doesn't actually battle... at least at first. She's too scared to brawl, but she knows the rules of Bakugan inside and out and is still useful to her friends as a strategist; they win many battles due to her suggestions.
If Alice ever wanted to battle, she could easily be the #1 Bakugan Brawler... and sure enough, that's exactly what Masquerade is. On top of having access to Alice's knowledge and strategies, Masquerade has the added bonus of knowing Alice's friends personally, giving him a further advantage.
6 Masquerade Is Connected To Hal-G, An Alter Ego Of Alice's Grandfather
Masquerade is the hands-on villain who the Battle Brawlers have to deal with for most of the series, but he answers to higher powers. One of them is Hal-G, a green-skinned demonic man, who in turn is a servant of Naga, a power-hungry Bakugan who lacks a type. Hal-G is the alter ego of Alice's grandfather Michael, which the heroes discover when a video recording Michael left in the lab features him transforming into Hal-G.
A silent Masquerade is seen in the background of this video; it turns out that Alice was visiting her grandfather when Naga's energy transformed him into Hal-G and she was turned into Masquerade alongside him.
5 Masquerade & His Minions Always Know Where The Battle Brawlers Are
In Episode 14, "The Story of Vestroia," Masquerade decides to level the playing field and recruits a team of his own. He invites the top brawlers in the world (those not already aligned with the heroes) to visit him, then brainwashes them into his servants. He also equips them with Doom Cards, the cards which send losing Bakugan to the Doom Dimensions.
No matter where the Battle Brawlers go, Masquerade and his minions are able to follow them; the logical conclusion is that he has an inside person on the team. This is a hint that even the Battle Brawlers themselves catch onto, not that it does them any good in actually determining Masquerade's identity.
4 Runo Previously Thought Alice Was *Working For* Masquerade
Continuing on from the above hint, Runo eventually decides in Episode 25, "Trust Me," that Alice is the most likely candidate to be working for Masquerade. The others are resistant, but Dan admits that the evidence isn't in Alice's favor. When Alice helps Dan and Runo win a battle, the bonding moment erases doubts.
The episode is both foreshadowing and false reassurance for the viewers. It raises the possibility of a connection between Alice and Masquerade, then shoots it down. The episode even has scenes of Alice alone, hurt that her friends believe this; no spy would be doing so, and that's because Alice doesn't know she's Masquerade.
3 Masquerade's Outfit Conceals His Chest
This is only a retrospective hint, and one concerning the elephant in the room: the gender aspect of this twist. The show glosses over this; after all, explicitly trans characters are something cartoons now are reticent to have, let alone ones made in 2008.
Still, Masquerade is essentially a trans boy, with his mask being the easiest gender affirmation surgery ever. Still, some of his outfit choices take on a deeper meaning after it's revealed that he's living in a biologically female body. His long-coat parts at the lower torso; above that are a pair of straps binding the coat to him. Beneath the coat, he wears a metal chest plate. It's clear Masquerade isn't doing this just for fashion, he's wearing these to hide Alice's very feminine chest. Whether he's doing it just to conceal his identity or suppress any dysphoria is a subtext the writers probably didn't intend, but adult fans can speculate on.
2 Alice Doesn't Go To The Doom Dimension Or To Dan & Masquerade's Battle With The Others
Related to the point about Alice and Masquerade never being in the same scene, Alice is conspicuously absent from some important scenes that feature Masquerade; scenes where all the other Brawlers are present. Some of them include Dan's battles with Masquerade in Episodes 27 "Showdown," and Episode 38, "Behind The Mask Of Masquerade."
She also doesn't go to the Doom Dimension to retrieve Dan and Drago, yet when the Brawlers return, she starts going missing. That's because Masquerade takes his own trip to the Doom Dimension...
1 Masquerade Fights An Apparition Of Alice In The Doom Dimension
This is easily the most overt hint; the show tips its hands a few episodes before the reveal happens. When the Brawlers went to the Doom Dimension, they each had to battle an avatar of their self-doubt to emerge stronger. When Masquerade faces his own challenge, it comes in the form of Alice.
The two have had, as has been mentioned, no previous interaction or relationship. Alice being "what [Masquerade] must overcome" only makes sense if there's a deeper connection that the two of them share, one viewers haven't been privy to.