(Something I'm going to do before i make my reviwe on Hyrule Warriors. And yes i'm still going to do that.)
Hijacked by Ganon is when a new villain is revealed to be working for or is a pawned of a already established villain. In stead of a new villain being behind a old one.
Note that this trope is not inherently bad. As it's sometimes better to uses a villain that the audience is already familiar with rather then make one up at the lest minute. This is also common for fan favorite villains to keep reappearing and take over the plot.
Several times in The Legend of Zelda series the hot new Big Bad turns out to simply be a pawn of Ganon or is trying to revive him. Notably, most of these games also feature the Master Sword.
A Link to the Past features an odd, ambiguous situation due to the fact that main villain Agahnim is said, depending on version, to be either a pawn of Ganon or purposely working for him,note It's also stated fairly early on that his goal is to free Ganon, rather than being a plot twist yet Ganon directly refers to the dark wizard as his own alter ego right before the final battle (which is supported by an image of Ganon's shadow popping out of Agahnim's body, turning into a bat, and then flying into the Pyramid of Power). If such a claim is indeed true, Ganon quite possibly hijacked ALttP from himself.
In the Oracle games, the Twinrova sisters, Kotake and Koume, are the real Big Bads. Ganon is the Final Boss, but he does not directly have a hand in the plot, making him more of a Bigger Bad.
Four Swords Adventures is a odd mixture of this and The Man Behind the Man. Vaati is a reccurring villain from the prequel game, and is further established in an earlier prequel, but about halfway into the game we find out that Ganon is the true villain of the story, just using Vaati as a decoy. In this case, Ganon hijacks the game from the newer villain Vaati, but Vaati was already an established villain as an alternate to Ganon, so Ganon becomes The Man Behind the Man as well.
Then there was Zant of Twilight Princess, who, after being built up as "The Twilight King", became the victim of yet another twist hijack by Ganon. While this caused a lot of debate, it was already known before the game came out that Ganon was going to be in the plot and Zant does allude to Ganon being behind him the first time you encounter him.
Played with in Skyward Sword, as Ganon doesn't appear in person, but the ending reveals that the spirit of Ganon that keeps pursuing Zelda and Link's descendants is the incarnation of the hatred of Demise. Thus in an ironic twist, everything Ganon has done has been essentially hijacked by Demise. Also counts as Fridge Brilliance as Demise doesn't mention Ganon by name. This not only explains how Ganondorf can be the same character in multiple games yet sport different visual designs, and have different Ganon forms, but also implies that other, unrelated Zelda villains could also be Demise, most likely Malladus from Spirit Tracks. It also adds an extra layer of intrigue to possible future Zelda villains who don't lose out to Ganon that game/timeline.
In The Legend of Zelda: A Link Between Worlds, it's actually inverted. Yuga first appears to be the Big Bad, but then Ganon enters the picture, revived by Yuga. Just as you expect him to take the position of Big Bad, Yuga absorbs Ganon's power and merges with him before he can do anything. Then Hilda is revealed to be the woman behind the man all along, and you think Yuga's role as Big Bad is going to to stop there, but he actually betrays Hilda, turns her into a painting and absorbs her power, once again keeping his position. Hijacked by Yuganon, indeed.
Zig-zagged but ultimately played straight in Hyrule Warriors. The apparent Big Bad at the start of the game is Cia, a corrupted witch and Anti-Villain. It's soon revealed that the driving force behind her corruption was none other than Ganondorf himself. However, his initial attempt to hijack the plot is thwarted when he tries to pull a You Have Outlived Your Usefulness on Cia, only for her to turn the tables and banish him with the Triforce. For awhile it looks like Cia's going to be the Big Bad after all, but Ganon takes advantage of her conflict with the heroes to restore his full power and promptly takes over again after she's dealt with.
This is Dr. Wily's trademark tactic in the Mega Man (Classic) series.
In the Batman Arkham Series, The Joker is always the real Big Bad.
Five Nights at Freddy's 2 introduces newer "toy" counterparts to the animatronics from the first game. After about two nights of fending them off, the older ones come out and start hunting down the player's office, far more aggressive than the new ones did. Meanwhile, all of the toy counterparts save for Mangle (the new Foxy) stop attacking almost entirely until the bonus nights.
n Jak 3: Wastelander, it's revealed that Errol was turned into a cyborg and is working with the Dark Makers.
Kingdom Hearts, thanks to its confusing cosmology, has a rather weird example: the Big Bad of the entire series is Xehanort, but he appears in many different incarnations over the series, and these incarnations repeatedly pull this trope on the other villains.
Both seasons of Ben 10: Ultimate Alien used this trope:
Season 1 featured Magnificent Bastard Aggregor as the main antagonist, whose scheme remained unstoppable for most of the season...then, when it was about to succeed, Kevin sacrificed his sanity by using the part of his power that would cause him to go crazy again to stop him. After he is defeated, Kevin, now back to being a psycho, serves as the main villain for the remaining episodes of the season.
Season 2 is even more complex; it starts with a Big Bad Ensemble involving a war between the Forever Knight and a new, mysterious sect that turns out to be manipulated by Ben's Arch-Enemy Vilgax. Then an Eldritch Abomination Vilgax had been impersonating shows up and takes Vilgax as his Dragon, apparently becoming the new Big Bad... until Vilgax betrays him, absorbs him and becomes the final villain of the season.
Season 3 of Jackie Chan Adventures has the Season's Big Bad, Daolon Wong, resurrecting Shendu in order to obtain the wayward Dragon Talisman power. The results are obvious.