It happens more often than you think, especially with regards to the themes of parenthood and 'the son becoming the father' principle. Here are just some examples of how, if you consider all of the variables, these villains were in fact ultimately doing the right thing. Some might have We start with the first three on our list (in no particular order!). It should go without saying but SPOILERS AHOY!
Assassin's Creed III
Ubisoft
(2012)
Shay teams up with the Templars once he learns that the New World Assassins are planning to use an ancient device to dominate the Templars and then the world, and together they manage to take out all of the major Assassins who were in on the plan. Haytham Kenway, the Templar Grand Master sent to the colonies in order to extend the Templar Order, leaves Achilles alive but wounded as a personal favour to Shay. Years later, the events of Assassin's Creed III would transpire when Haytham's son, Connor, seeks out Achilles in order to get revenge after a Templar-led attack resulted in the death of his mother and several of his people in the forest. Whilst Haytham's involvement in the murder of Connor's mother is slight (as it was in fact the Templar Charles Lee who led the assault in the forest), he does try to sway Connor to the side of the Templars - citing, albeit obscurely, Achilles' actions in his youth which cost him his entire brotherhood. Ultimately whilst Connor decided to follow his own creed for vengeance as opposed to syncing directly with either of the two feuding Orders, it could well be argued that Haytham's actions, as well as his vision, for the population of the New World was a far safer choice than that of the Assassins (who had sought to take world peace by force). Connor actually agreed and the two became allies briefly. The Templar's plan wasn't to use ancient technology, but rather to replace President George Washington with a Templar agent the Order could manipulate, leading America down a different and much less 'chaotic' path than it eventually ended up following. Unfortunately for Haytham however, the Templar agent he specifically had in mind was the same man who murdered Connor's mother. His alliance with Connor collapsed when Connor ignored his pleas, driven by vengeance, killing his father in pursuit of Charles Lee.
Whilst Haytham's plan for America never resurfaced in the years after, it was his actions which saved the colonies from complete destruction. That's not to say he was at all pure of character. As a Templar he was a severely ruthless human being and all in all an utterly terrible father figure, but it was all - arguably - for the greater good.
BioShock Infinite
Irrational Games
(2013)
After an inter-dimensional odyssey across space and time, Wounded Knee veteran and former private investigator Booker Dewitt is presented with a terrible truth by his faithful companion, the mysterious girl who had been held captive on the floating sky city of Columbia, Elizabeth. Amongst learning other revelations such as that Elizabeth had, in fact, been born as 'Anna' and was abducted from her own world as a baby, Booker also learned that it was all due to a choice he made before the events of the main game where he gave up Elizabeth thus 'bring us the girl and wipe away the debt.' Booker also learned that the man responsible for abducting Elizabeth was actually a deeply religious (and heavily racist) version of himself from an alternate timeline where he had himself baptised after the Battle of Wounded Knee, whereas in Booker's own timeline he refused the baptism. This means that Booker DeWitt and Father Comstock are the same man in two seperate timelines. In Booker's timeline, he never forgave himself for what happened at Wounded Knee, had Anna later on in his life, got addicted to gambling and gave her up to 'wipe away the debt.' Whereas in the other timeline, Booker was baptised and became a new man in order to forget the 'sins' he committed at Wounded Knee. He forged his own religion based on American Christianity and sought to invest in inter-dimensional travel. This led to him being able to construct technology far, far out of its own time, leading to the development of Columbia (amongst other things). Ultimately, Comstock's exposure to this technology aged him and rendered him sterile. Realising this his body was being slowly destroyed as a result, Comstock needed an heir to inherit Columbia and its people once he passed away. With help from Lutece and his own inter-dimensional twin, Comstock located an alternate version of himself in a parallel world who had a daughter.
See? I told you to bear with me.
Final Fantasy X
SquareSoft
(2001)
So Final Fantasy X sees the protagonist, Blitzball prodigy and pronounced girl/boy Tidus, sent forwards in time by a thousand years. He explores the ruins of his former world and discovers that the advanced technologies of his era was all but laid waste to a great war during his absence, at the end of which a giant monster called Sin emerged. The future world is known as Spira and whilst certain things remain, such as swords and Blitzball as a sport, Tidus finds the descendants of his friends to be almost wholly religious, following the strict lifestyle of Yevon. Yevon dictates that Summoners (individuals of great power, accompanied by companions) must pilgrimage across the land, allying themselves with ascendant creatures known as Aeon, in order to defeat Sin and bring the Calm (a temporary period of peace) to Spira. Tidus becomes the companion of one such Summoner named Yuna, the daughter of the previous Summoner who brought the Calm across Spira. Tidus also discovers that his father, who had also gone missing from his own time, had also been transported to Spira and that he too was amongst the companions of Yuna's father during their pilgrimage several years prior.
If that sounded complicated at all then here's the simple bit. So in order to defeat Sin, a Summoner has to sacrifice their life during the Final Summoning (whilst battling Sin from the inside) as they will summon the Final Aeon (comprised of the soul of a trusted companion) which will then kill the Summoner and become the next Sin. This means that Sin will eventually come back to Spira in the months after its defeat to end the Calm, empowered by the soul (or 'Fayth') of the dead summoner's companion. On this particular occasion, it was Jecht who chose to sacrifice himself. This meant that it was Tidus's father, not Yuna's, who 'became' Sin in the events of the last pilgrimage. This means that the Sin who appears throughout Final Fantasy X is in fact the protagonist's father, who cannot control the actions of the mindless beast his soul is keeping alive. This of course results in Tidus and Jecht facing off with one another. A series of circumstances results in Tidus and Yuna and the other companions discovering that the reason for Sin's continuing resurrections is shrouded in conspiracy, at the heart of which is Yevon, meaning that the religion Spira is dedicated to is actually the harbinger of its own misery (and is thus directly responsible for the deaths of thousands and thousands).
Okay, so maybe that was even more complicated, but as a JRPG it was bound to be really. In layman's terms, Sin is actually Tidus's father who sacrificed himself in order to bring peace to Spira and save hundreds of lives in the process.
Part Two - Coming Soon!
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