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IN-SERIES ANALYSIS
Before he went villain, I’d say that Varian’s feelings toward Rapunzel were more hero-worship, so he likely thought she was pretty, but undoubtedly out of his league and already taken to boot. No signs of crushing yet—he instead becomes infatuated with the only unattached person who came to visit him: Cassandra.
In my humble opinion, Varian didn’t have a romantic attraction to Rapunzel until it hit him like a bolt of lightning when she told him “It’s your mess, but it’s my kingdom” in Rapunzel’s Return.
Though he was oddly flirty with her while she was in that dungeon cell...
There is also the distinct possibility that the cell was where the first stirrings of a crush began to form during their reconnection. The basis for this theory comes from the absolutely adoring look he gave her when she said “we need him” and how he looked pretty well smitten as she pulled him along.
By the end of the episode Rapunzel frees Quirin, and hoo boy, is that the final nail in Varian’s coffin of feelings. She’d forgiven him his atrocities, kept her word, freed his father—honestly, it’d be weirder if he didn’t fall for her if you ask me.
Then Be Very Afraid rolls along, and we learn that Varian considers Rapunzel “wondrous and magical,” something Rapunzel notes rather slyly and Pascal seems to think is sweet. The look on Varian’s face when she takes his hand and pulls him along again says it all. Boi is smitten.
Additionally...just look at this dork when Rapunzel catches him being a nerd about metals and drinking hot cocoa in Cassandra’s Revenge. This is the reaction of a teenager who just got caught doing something embarrassing by his crush. He zeroes in on Rapunzel specifically and doesn’t seem to care that any of the others caught him.
But through all of these new feelings for Rapunzel, Varian loves Eugene too (90% platonically in this case), so my take is that he’s resolved to not interfere in their relationship. And after everything that’s happened, he likely feels that Eugene is a better match for her and that they truly deserve each other. Though after his stint as a villain where Varian completely lost his respect for the ruling class, the whole “she’s a princess I’m a peasant” thing would likely not be a factor for him anymore. Also, he’s clearly never given a crap about age gaps, and the 4 year gap between him and Rapunzel is even smaller than his canonical S1 crush on Cassandra with an 8 year gap.
Now that we’ve covered the analysis of canonical events, we can delve into pure fanon speculation territory.
POST SERIES SPECULATION
While Varian has indeed resolved to not do a single stupid thing to mess up Rapunzel and Eugene’s relationship, he can’t keep himself from wanting to be close to Rapunzel and craving her affection. Luckily (or unluckily, depending on how you look at it) Rapunzel is a very affectionate person, so she’ll hug Varian, hold his hand, even cuddle him because he’s her precious friend. Also, she’s a pro at giving him the verbal validation that seems to fuel him (aka his love language: words of affirmation).
This results in Varian coming up with excuses and ways to stay close to Rapunzel, and at times when he ends up being sandwich-snuggled between Eugene and Rapunzel (because let’s face it, we’ve seen that Eugene is huggy) he sometimes catches himself trying to pretend Eugene isn’t there, which he instantly feels super guilty about.
Side note: Ruddiger is completely aware of how he feels because Varian is an open book when he’s alone with his little raccoon buddy, and the devious little critter sometimes manipulates situations to try to get Varian alone with Rapunzel or to set them up for what he believes is a romantic encounter (what do you mean being trapped inside a dumpster together isn’t romantic? Intimate dark setting, and all the garbage you can eat!). These setups only work about half the time, and so while Varian appreciates the sentiment, he’d prefer Ruddiger to stay out of it because the failures tend to end with Varian being horribly embarrassed.
And if Rapunzel ever gives him what she views as chaste kisses on the cheek or forehead, Varian’s over the freaking moon and always blushes so hard he almost passes out. Rapunzel finds it cute while Eugene thinks it’s the funniest thing ever and teases Varian he’s gonna have to get over that habit if he ever wants a girlfriend/boyfriend of his own. Whether he’s aware of Varian’s crush or not is up for debate, but he for sure has no idea how deep it runs and thus considers it harmless if he’s aware of it.
Varian probably also frequently gives Rapunzel gifts in order to get her attention and favor in the form of inventions/discoveries he thinks she’ll like. He might even bake her things since we’ve seen he has a knack for it. His favorite thing is if he can get Rapunzel to come work on a project with him, giving him the one-on-one time he craves while doing something he loves.
Also, I think that if anyone were to insult Rapunzel in Varian’s presence, they might find their shoes sticky bombed to the floor. Looking at you, Uncle Monty. Varian might become the second person in Corona to not like him.
Of course, he’s not so obsessed with Rapunzel that he has no life outside of her, since he very much enjoys one-on-one time with both his dad and Eugene (Lance is kind of a 50/50 shot for him, and the girls are like little sisters to him). And of course he spends most of his time in his lab doing alchemy. But he lights up every time Rapunzel enters the room and gravitates towards her, and would do pretty much anything for her.
And for a while, Varian convinces himself that this is fine, and that he doesn’t need Rapunzel to love him back the same way he loves her. Though he feels small flares of jealousy whenever she and Eugene kiss or indulge in other romantic gestures that Varian would never hope or dare to try, but he stomps the jealousy down for the greater good of everyone involved.
The wedding would be super bittersweet for him, since he’d be so happy that his friends have found happiness together, even while knowing that Rapunzel is unquestionably out of his reach now. But that doesn't stop him from continuing to love her. His dad says he’ll get over her one day (his only human confidant, the dude is legendary at keeping secrets), but Varian isn’t so sure.
And from this point, the fanon possibilities are pretty much endless, some of them running the gambit from Varian continuing to respectfully pine for Rapunzel in secret, to him getting over her and finding his own happiness with someone else, to him gradually descending into madness and going just a touch yandere. Depends on what flavor of Varian you’re in the mood for: pining Varian, happy Varian, or villainous Varian. And of course, you can get real fancy and combine different Varian flavors to make something unique!