SO, after watching today's epiosde's A;an is really a total dick like he may not not the full extent of Team Flare's plan but he freakin saw ZYGARDE BEING ZAPPED WITH A GUN AND PUT INTO A CAGE AND SAID ABSOLUTELY NOTHING OR EVEN THINK IT WAS WRONG. How can you still say that Alan isn't somewhat a villain, it not just about "being confused" or "helping to recover hari-san".
I’m a bit disappointed over the lack of explicit contextualisation (they had done it well in XY&Z013 with the short moment of dialogue between Alan and Fleur!), while here we didn’t follow Alan’s point of view at all this episode, but: 1°) Alan is confirmed to not be working with Flare (the Admins really weren’t expecting him to be there, and Alan did confirm he was there because Lys had asked him), 2°) re-used animation is Not Unusual (and understandable), but CLEARLY, the fight against Zygarde was choregraphied to echo the fight against Groudon from Act III where The Two Legendaries were just big bad news (I would like to hear it explicitly, it’s an assumption from me at this stage, but I really really wouldn’t be surprised that Alan, right now, sees all legendaries as threatening due to Kyogre and Groudon’s actions. He arrived just when Zygarde 50% was on the verge of launching an attack on some ‘mon and given the hits Lizardon took, I’m not sure they would have survived?), 3°) anyway, Alan doesn’t know what TF is doing or aiming at. He helped Lys, because he trusts Lys to do the right thing (and Lys has never mentioned anything about threatening the world or harming people to him).
So Alan is more a big, big idiot thinking he’s globally helping people by helping Lys (he’s not even assisting him in genocide/world domination/whatever, he’s helping him for research, for preventing ~bad people~ from using their discoveries, and for putting sources of power away from legendaries who would cause problems + the whole Hari-san deal in the background). That he helped with catching Z2 is indeed a bit weirder, but it wasn’t even “terrified”, it was pissed, and people in that word tend to catch Pokémon by brute strength; if Alan knew about the experiments that were done to Puni-chan in Act IV, it would be another story, but he precisely doesn’t know that Lys will do something harmful to it or to Humanity (so far), so /o/
He’s not doing good things, but he’s not gleeful about it, not exactly enjoying it, and he’s basically lacking the context. N in the games was much more problematic (he was bred into it, he lacked some bits of knowledge, he didn’t know Ghetsis wanted to double-cross him, but he was still really fervent about doing a coup d’État and forcing people to release their ‘mon whether they wanted it or not), and I wouldn’t call him a villain, so I have even less reasons for Alan /o/
(But he does make Terrible Decisions, and was a dick to Manon, THAT is for sure.)