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Naboo is being overrun by Sith troops (for arguments sake Sith troops have upgraded weapons to Clone Wars standards). Obi-Wan and Qui-Gon face Malgus instead of Darth Maul. Who wins this fight?

To make it interesting, Palpatine aka Sidious does not exist. The Republic is at war with a reborn Sith Empire. Malgus is the overall commander of Sith forces

so it's TPM Kenobi?

Malgus dominates in my opinion. He could dispatch Kenobi with some lightning and then overload Qui-Gon's defenses with his offensive saber style.

I'm with Mizukage on this one. Malgus is too formidable on the physical level.