Sonic the Hedgehog has been around long enough at this point for fans to fall into generational gaps, stratified like layers of sediment. The Sonic fan of 1995 has different memories of the franchise than that of 2012, and both of them would have some interesting differences from the fan of the modern-day.
Sonic the Hedgehog 2 is following one of the most successful and beloved video game adaptations of all time with some hugely beloved characters coming to the screen for the first time. Miles "Tails" Prower is still Sonic's lovable sidekick, complete with his in-game voice talent intact, but Sonic's other companion seems a bit different.
Knuckles the Echidna has been all over the trailers of the upcoming film. Fans are immensely excited to see the two-fisted monotreme finally make his big-screen debut in the sequel, but he seems to be in a different role. Knuckles faces off against Sonic in pitched combat, chases him down the mountain on a snowboard, and punches him through several solid objects. Robotnik is still the main villain, but Sonic seems to easily defeat the encroaching robot hoard. Knuckles seems to be a much bigger threat for the Blue Blur. This might come as a shock to some Sonic fans who've only ever seen Knuckles be the muscle on the hero's team. In the Sonic Boom cartoon, or in most of the current games, the red echidna joins Sonic in his battles against Robotnik. So why has Knuckles taken Robotnik's side in this conflict?
Knuckles was introduced to the franchise early, only three years and four games in. Sonic the Hedgehog 3 and its expansion pack Sonic & Knuckles were the first appearances of the character. He was so immediately popular that he got his own spin-off shortly thereafter, and he has remained a key part of the Sonic canon ever since. He's been a playable character in a ton of mainline Sonic games, from Sonic Adventure to Sonic Mania. In the classic team-up game Sonic Heroes, he's a part of Sonic's main team, as he has remained in almost every other property. The Sonic Boom game and animated series added Amy, making Knuckles a part of the main four. Even when he isn't playable, he's almost always cheering Sonic on or helping out in the cutscenes. All this becomes interesting because his very first appearance, back in 1994, saw him as one of the bosses.
In Sonic 3, the brief and wordless cutscenes tell a story that appears to be the basis for the new film. Knuckles lives a quiet life, guarding the Master Emerald on his floating island home. His dutiful watch is interrupted by Dr. Robotnik's sudden fall from space. Robotnik is saved by the well-meaning but foolish Echidna and immediately begins to manipulate him to his own ends. Robotnik convinces Knuckles that he was attacked by a blue hedgehog and that the same speedster is on his way to steal the Master Emerald. Knuckles trusts this claim immediately and hunts down Sonic, attacks him, and steals the series' favorite MacGuffin, the Chaos Emeralds. Now that its guardian has departed, Robotnik immediately takes the emerald and relaunches his orbital weapon, the Death Egg. Knuckles serves as an antagonist for the entirety of his first appearance, entirely thanks to the meddling of the true villain, Robotnik.
By the time of Sonic & Knuckles, Knuckles became a hero. Sonic sets him straight, proves that Robotnik is tricking him, and the trio defeats the mad scientist together. Knuckles' career as a villain lasted one game, and his career as a hero began immediately thereafter. Other works in the franchise have introduced the character in similar ways. He appears in the early 2000s cartoon Sonic X in much the same capacity; tricked by Robotnik, briefly fights Sonic, immediately turns on the bad guy, and joins the heroes. This introduction serves a few purposes in the narrative. It establishes that Knuckles is comparable to Sonic in terms of sheer power. It establishes that Knuckles is well-meaning, but typically pretty dumb. It's a simple misunderstanding that lets two characters fight it out with no hard feelings at the end. The film, however, could have a slightly different direction.
The Sonic the Hedgehog movie established a different backstory for Sonic, seeing him travel from another world to avoid capture by enemies. The enemies that chased him and slain his caretaker were masked Echidna warriors. Some of Knuckles' dialogue mentions his background as a proud warrior, another line sees him decry Sonic as "unskilled, untrained, unworthy". It seems as if Knuckles' motivation might be related to this Vegeta-esque hatred over Sonic's use of his powers. While this new factor will almost certainly play a role, Knuckles is being strung along by Dr. Robotnik, just like he was way back in the 90s. That being the case, he'll probably be back on the good guy team before too long.