Admiral Haruki Kusakabe from Martian Successor Nadesico establishes himself as a very detestable person near the end of the TV series, by framing Tsukumo Shiratori for treason and having his former best friend Genichiro "mercy-kill" him, all in order to prolong the war between Earth and Jupiter and have a chance to seize Mars' forgotten technology. He is finally discovered and forced into exile, but plotting revenge...and what marks his real entrance into Complete Monster territory is the fact that, in the three years between the series and The Movie, he had Akito and Yurika captured and experimented on to replicate the Boson Jumping effect. The experiments permanently hooked Yurika up to a machine, in a catatonic state, and completely destroyed Akito's senses, leaving him an empty, tragic shell of the innocent boy he was. He's also a Karma Houdini, so it's even more infuriating...and it makes it even more cathartic when you get to kill him off in some Super Robot Wars episodes. Preferably with Akito and Gai's Double Gekigan Flare...
His Karma Houdini status would have probably been undone in the sequels, but, since Word Of God is they've all been cancelled with no chance of ever being made...
There is also Yoshio Yamasaki from the same movie, the Martian Successors' resident Mad Scientist who was directly responsible for doing all those horrible experiments on Akito, Yurika, and Lapis - and possibly on a lot more people before them. This guy is the most chilling character in the whole Nadesico series: there is something about his cheerful and friendly demeanor, even as he's committing all those atrocities, that only manages to make him more horrific. It's not that he enjoys his cruelty. He just has no feelings whatsoever about it. To him, ruining countless people's lives or mind-raping an innocent girl into becoming a mindless machine is just as mundane as brushing his teeth in the morning. Think about it - he won't even have his conscience to answer to; he has no conscience, period. He's just pure intellect unbrindled by emotion. Think an evil version of Lloyd Asplund, make him a hundred times worse, and you've got Yamasaki.