Liberator of the Council

In S1 both were still young and finding their footing, but mainly Emma. Daniel had already dated Maddie for a while and then went through the whole first season flirting and liking Emma after his break up with Maddie. Daniel was also on top of his game, being the Sharks Swim Captain, and other than Maddie being his girlfriend, his life was happy and fine. Emma coming in merely improved it, she was nicer, thoughtful, and down to earth. But Emma's story was just beginning, she was discovering being a witch, having to deal with her powers, a witch bully Maddie at school, and daily shenanigans that entailed the magical world. Daniel is the last person to discover Emma is a witch and he also has the worst reaction to it. Not that surprising considering how regular his life has been, but that kind of tells us where this was headed.

In S2 Emma and Daniel have been together for months now, all through the summer. The thing is, Daniel's been happier than ever and he thinks Emma's powers never came back, something that she's been hiding from him this entire time. Lying to your SO is never a good thing, especially about something this big, something that is literally part of you. There are reasons for both of them however:

Emma knew how happy Daniel was that she was 'regular' and didn't want to ruin what they had by bringing in all her witch stuff, which tended to bring all sorts of chaos and antics.

Daniel didn't want Emma to have powers out of fear that other evil witches would come after her because she was the Chosen One.

While these are reasonable explanations for both of them, they're not fixing any of their real issues. Emma should not be lying to her boyfriend, eventually, it did catch up to her and she tried using magic to make him forget. Also not a good thing, even if she wanted a 'redo' at telling him. When he does find out, it causes their downfall. The thing is, Emma lied because Daniel just can't handle her being a witch. He's said that her powers being back would "ruin everything" and has shown a fear of witches when magic was brought up in S2E05. Emma keeps telling him that powers or no powers, she's still a witch. Still, she chose to hide a part of herself to try to have a normal relationship with her boyfriend. But hiding a part of yourself is never the answer and it eats away at you.

S2 also explores the fact that witches can't date humans, it's not allowed. The Council tries to have Emma break up with him otherwise they must take the witches magic away, but Emma being the Chosen One is a special case. Her magic removal is not on the table and she wants to keep her powers regardless. (I mean I agree with Emma, let the girl date whoever she wants) But it is another thing that drives them further apart, unfortunately, the Council ended up being right, most humans just can't handle the magical world. (Andi can handle it, so can Katie and Sophie, but Daniel can't.)

When it comes to the Fool Moon, it has a different effect on all sorts of witches. Jax's greed and envy magnify, Desdemona turns vindictive and wants Emma's powers, and Emma's impulse control is gone. This leads to Emma casting spells without really thinking about the consequences and out in the open. The Fool Moon is just a witch or wizard's desires coming to the surface. In retrospect, Maddie was just as affected, she started improving (slightly, but still progress) and didn't run from her feelings toward Diego. She was more open and entered a relationship with him.

We also see Emma's clones in this season. Her first clone, E, encompasses her dark side with none of the good. She calls Daniel dull, she's bored with him and his ideas for dates, and she finds Jax fun and wants to do magic whenever she wants. She's happy when Daniel breaks up with Emma because 1. She found him boring and 2. They get to keep their powers now and the Council can stop hounding them. This may be Emma's darkest side but it's still Emma. Some part of her does believe that Daniel is dull and finds Jax fun. Granted, her third clone, the Nerdy Emma is all about Daniel. This is why the clone spell is so very illegal, a witch is essentially pulling out a part of themselves and without the rest to balance it, they become a paragon of just one emotion or drive or aspect of their original personality. They're not whole. The Real Emma shares all these traits inside herself, she does like Daniel, she does find him dull sometimes, she does like math, she does find it boring at times, and she does like Jax but she does think he goes overboard sometimes.

See, this is where we come into an important piece of dialogue in S2 E16 between Maddie and Daniel talking about their romantic troubles.

Maddie: But if you two were still together, you'd want her to stop using her powers? Daniel: Maybe. Maddie: Then you don't accept Emma for who she is. And as a fellow witch, I'm offended for her!

This is an interesting moment in which someone like Maddie, someone who doesn't like Emma but is a witch just like her, sees that while Emma lied to Daniel, she did it because Daniel doesn't accept her as who she is.

Daniel has openly expressed anger and disinterest at the magic world. And hey, I understand, after all the spells Jax has cast on him to make him look bad in front of Emma's dad, or just the usual magic hijinks from Emma or Maddie, magic is not Daniel's friend. He doesn't find it fun or cool like Andi, he's not desensitized to it like Katie and Sophie. He's suffered from it and doesn't want anything to do with it and hey I can respect that. But this isn't good when you're in a relationship with a witch, the most powerful one in fact. So he's tiptoeing a line constantly between wanting to be with his girlfriend but disliking and fearing something that's part of her (and part of his friends' lives: Maddie and Diego).

Let's get to S3 when he was marked by Mia with her Kanay spider. Spider!Daniel broke up with Emma, started dating Mia, was a general jerk at school, even tied up his little siblings. It turns out that Mia's Spider doesn't cause him to act strange or evil, it just unleashes someone's 'inner wild'. It makes them do what they most want to do. So, Daniel did want to break up with Emma. He called Emma and Maddie trouble-brewing witches and had no problem telling a complete stranger all about their powers.

Now we could get into how Daniel's life was turned upside down more than plenty of times because of magic, but nothing beats S4 when Emma literally rewrites time when Daniel disappears. He and his family end up running an animal sanctuary and dating Mia. Then his life gets put back and it's for the worse because now he has no animals, no girlfriend, and he's back in a school hated by the principal. Overall, Daniel was not having a good time in S4. One of the many reasons why Emma puts him back where he was happy. (I would also like to remind everyone that Mia and her previously deceased parents were alive in the new accidental timeline of S4. I believe that Emma also was the cause of this, not only did she unintentionally give Daniel a better life but the same to Mia. And then she restored that life at the end of the season.)

In conclusion, Jemma forever.