Throughout fifteen seasons of following the Winchester brothers saving people and hunting things, Supernatural was constantly trying to surprise its passionate audiences and justify its longevity. Multiple times the show changed things up through Jack Kline's introduction, Mary's resurrection, and shifting the focus of the mythology, so of course, plot twists were used to keep things fresh.
Twists like John's death, the fall of the Angels, Sam's first death, and more breathed life and a sense of surprise into the show, but not all plot twists were as out of nowhere as those, many were seen coming by a lot of the fans.
Jack Is Good
The build-up to the arrival of Lucifer's spawn, the Nephilim Jack Kline, was full of speculation from characters and fans alike over whether or not he would follow in his father's footsteps or if he would be good.
Not every fan would have thought Jack would be good, but it becomes clear in the build-up to his arrival. Castiel's newfound and unwavering confidence in Jack's goodness after seeing a vision of his future was a big step in confirming how good Jack would be, especially when combined with the motherly love from Kelly. Jack could easily have been made a villain, but it would have felt a bit unfair to Cas and Kelly, and with Lucifer alive, it was pretty clear the two would not join forces.
Lucifer Wants To Use Jack
The entire plotline of Lucifer getting a woman pregnant in the first place was quite a shock, especially considering the wild circumstances of him being President of the United States. Despite him disputing the claims, Lucifer was always going to use Jack for evil.
Lucifer tried to convince people he truly wanted to be a father. He even resurrected Sam and acted peacefully with the heroes in the alternate world. However, he revealed himself to be just wanting to use Jack fairly quickly. Lucifer wanted his usual big bad goals of total death and destruction, world domination, and to get a bit of payback against his dad. Most fans saw it coming a mile away.
Michael Does Not Give Up Dean's Body
Back in season 5 of the show, Lucifer got to posess his perfect vessel in Sam, but Michael had to settle for Adam, unable to get the yes from his true vessel, his sword, Dean Winchester. Alternate Michael, though, did. Dean gave the yes so that AU Michael could defeat Lucifer.
After the two fight and Lucifer is killed by Michael, the heroes, for some reason, expect alternate Michael to free Dean. As could be telegraphed the moment Dean said yes, Michael refused to give Dean up as his sword, taking the power that he got from the Winchester to go do some harrowing experiments on monsters.
Jess' Death
The Supernatural pilot is such a fantastic introduction to Sam and Dean, but Sam makes it clear it is a one-time hunt throughout the episode. He wanted to get back to Stanford and Jess and leave Dean and hunting behind. The show had to get past episode one, though.
Jess's death was necessary to push Sam into hunting with Dean again, go after John, and be used in Azazel's grand plans. The manner of her death was debatable, and it maybe did not even need to be a death; perhaps a kidnapping could have sufficed. Jess being gone and out of the way was clear from the pilot's opening moments, though.
Bobby Is A Spirit
To many fans, Bobby Singer should not have died in season 7, especially not in how he died; a gunshot by Dick Roman. However, just because he died early in the season did not mean he was done. He came back as a spirit.
This is not a straight-up shock twist. It was built up and teased a lot, eventually morphing into more of a reveal. Fans are left with a cliffhanger in "Death's Door" as Bobby does not answer, stay or go to the reaper. It seemed clear to fans at that moment Bobby would stay, confirmed quickly by all the strange, spirit-esque activity surrounding Sam and Dean.
Cas Turns Good
Introduced epically in season 4, Castiel quickly became a fan-favorite but remained on the side of the less-likable angels for most of the season. It got teased throughout the season that Cas thought about disobeying Heaven, which finally came to fruition in "Lucifer Rising."
Taking Dean's speech about free will to heart, Cas betrays Zachariah and joins Dean in trying to stop the Apocolypse. It is a beautiful moment for fans of Cas, but one that everyone saw coming. Cas was never unlikeable, never positioned as a true villain like Uriel or Zach. He was good deep down, and it only took a classic Dean monologue to get him fully on the side of the heroes.
The Colt Can't Kill The Devil
When Lucifer got released from his cage in Hell, Sam and Dean, along with Bobby and Cas, scrambled for a way to kill the Devil somehow. While Cas relied on a hunt for God, Sam and Dean believed the Colt might be a route to go.
After getting the gun from Crowley, they set out to kill Lucifer before he releases and binds death. After finding him, Dean walks up to Lucifer and shoots him in the face with the gun. Lucifer then stands up and shakes it off, announcing he is one of five things the gun cannot kill. There was absolutely no way the gun would kill Lucifer, whether that be because the boys could not get a shot or because Lucifer is immune to it. It shocked nobody when Lucifer did not die halfway through season 5.
Sam Is Lucifer's Vessel
Early in season 5 of the show, fans find out that Dean is the vessel for Michael, the perfect vessel groomed for years to let Michael take a ride in him and destroy Lucifer. It got revealed later that Sam was the very same for Lucifer.
This is made clear early. The combination of Dean being Michael's sword and Lucifer obviously using Nick as a means-to-an-end made it clear that Sam was destined to let Lucifer takeover. Season 5 is widely regarded as one of the best of the show, so with its great writing, the reveal was by no means bad; it was great, in fact. But, it was easy to see coming for fans who knew about the intertwined fates of the Winchester's, and their often unhealthy co-dependency.
Resurrections & Sam & Dean Saving Each Other's Lives
It has become a joke amongst the Supernatural fandom that characters are always dying in the show. Not just minor characters, but all the main characters die at least once and come back. While many of the deaths and resurrections are shocking, some are painfully obvious.
The first deaths of Sam and Dean, as well as their first resurrections, are brilliant twists. But, when Sam is killed in the alternate world, or Metatron kills Dean, nobody believes they would not come back. There is also the ever-present plotline of the brothers putting the other's safety over the fate of the world, particularly Dean, and eventually, it became easy-to-spot. Dean saved Sam rather than shut the gate of Hell, and Dean killed Death rather than kill Sam. These sound shocking, but, in fact, were right in line with the characters and were always going to be the decisions made by Dean in the eyes of the fans.
Ruby Is The Worst
Debuting in season 3, Ruby was a fascinating character in Supernatural. Despite being a demon, it seemed she was a good guy, on the side of the Winchesters, especially in her first form. When season 4 rolled around, though, it became clear Ruby had ulterior motives.
The performance of Genevieve Padalecki and her getting Sam addicted to demon blood were clear red flags for Ruby in season 4. While it was definitely hard to tell in season 3, it became painfully obvious she was not on the good guy's side at all near the end of season 4, even if she did save the boys' lives numerous times.