It wasn't the HPV vaccine that saved the students.
A fan theory holds that it was actually Angelica's slime, which the unvaccinated kids didn't consume for reasons related to why they didn't get vaccinated – religion or “big pharma is evil”. Burr also had some slime (and a fallout shelter), while Crumble did turn into a ghoul and was only saved by her traumatic brain injury. The theory is also suspect because Burr advanced it, and as shown by his other actions, he cares about no one but himself; it seems pretty likely it was just part of his strategy to sedate and kidnap all the jocks and he never truly cared about why the kids are immune.
- Alternatively, it could be weed. Pretty much every character is seen having a blunt or standing next to someone smoking. Burr did have to handle confiscated weed as a director and Crumble was close enough with him to get some of the radiation surviving magic, too.
- Also alternatively: It was a combination of all three of them that allowed for them to survive. Maybe if it had been one or two items wouldn't have done it, but the HPV vaccine, Angelica's slime and weed lead to some accidental concoction that protected those who didn't turn.
- Alternatively, it could be weed. Pretty much every character is seen having a blunt or standing next to someone smoking. Burr did have to handle confiscated weed as a director and Crumble was close enough with him to get some of the radiation surviving magic, too.
Eli faked his death.
He overheard the new Daybreakers talk about another better mall and didn't want Josh to follow him. Josh will find him in season 2 whilest looting the other mall. Eli will be annoyed.
- Eli DID explicitly say he was the master of bluffing. And there wasn't any blood on the knife that supposedly stabbed him.
What we know of Sam in Season 1 is seen through "rose-tinted lenses" and her rule would end due to bad decisions.
Most of the story we get about Sam is from other people, like Josh, Angelica, Wesley. We never really get a clear sense of Sam's side of the story. If Season 2 had come to be, we would have found out that the entire time, she was a real selfish bitch who was putting up a front of niceness that everyone apparently everyone believed, including Josh. We would also find out she had sex with Josh because she was bored with their friendship, having started it to toy with him, and wanted to see how good he was. And when it comes to the scene where Josh snaps at Sam would reveal that Josh held up a mirror to Sam to show her exactly how horrible she really is. The bits where we see Sam alone after it's revealed that Josh snapped at her may have been Josh's idea on how she reacted due to how he interpreted their relationship (she may have not actually cried on her way to school or while getting prepared for Homecoming).Also, we would have discovered is that Sam's new job as ruler would have been short-lived due to terrible decisions and constant resistance from the Daybreakers. Most decisions she made while trying to stay alive in the apocalypse has been with others involved (like her just growing a garden to eat food) or have ended up drastically backfiring (i.e. freeing Mr. Burr and allowing him to take over because the kids "need an adult").
