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Now that we have seen a bit more of Vision's capabilities we now have more things to discuss about this fight.

Fight takes place in the airport where the big battle in Civil war was done. No humans around. Vision and Thor are out to destroy each other. For this fight, Vision is unable to wield Mjolnir (because I doubt anyone wishing Thor harm would be worthy of Mjolnir).

Discuss

Complete toss up IMO. We still don't know enough. If Vision's phasing is capable of harming Thor, then he takes this. On the other hand, we've never seen him phase-rip anything as durable as Thor, or show the level of damage output necessary to put him down. Conversely, we don't know if Thor has any way to harm him when phased, or the full extent of Vision's strength and durability. Electricity can clearly inconvenience him, however, which is rather relevant when fighting Thor.

Probably Thor. But like the above says, there's not enough info to know for sure.

I could see Thor just sticking the hammer into Vision's chest and then discharging lightning... Hawkeye's electro arrows seemed to give him trouble, Mjolnir is miles above that level.