The user can overcome their limitations/weaknesses, whether personal, from their species or inherent to their other powers, becoming either more resistant or completely immune to said weaknesses. This can be accomplished through ascendancy into a more divine-like state or natural evolution like performing repeated non-lethal exposure to said weakness; for example, a vampire may become immune to sunlight or a werewolf resistant to silver.
Red Stone of Aja (JoJo's Bizarre Adventure Part II: Battle Tendency)
Lapis lazuli (The Vampire Diaries)
Saya Otonashi (Blood+) has been able to control her blood-thirst through regular blood transfusions and eating large quantities of human food.
Son Goku (Dragon Ball) overcame his weakness to his tail being squeezed through extensive training.
When he still had a tail, Vegeta (Dragon Ball Z) was able to overcome the Saiyans' traditional weakness of having their tail squeezed.
Nappa (Dragon Ball) has overcome the Saiyans' weakness of having their tail squeezed, as Piccolo discovers the hard way.
Alucard (Hellsing) is immune to all vampire weaknesses except the most holy of Christian artifacts, such as Helena's Nail.
After entering Gear Fourth - Boundman, Monkey D. Luffy (One Piece) is able to retain his natural rubber state despite being coated completely with his Haki which should normally neutralize it, allowing attacks that would normally harm him to simply bounce off.
Saitama (One-Punch Man) broke through his human limitations after 3 years of training.
Due to its unique composition, the Crystal Onix (Pokémon) is immune to water and Water-type attacks, unlike other Onix.
The Frog Hermit (Ranma 1/2) has transcended the limits of his jusenkyo curse, allowing him to talk and fight as if he was still in his human form.
As he was originally human and turned into a vampire, Tsukune Aono (Rosario + Vampire) is unaffected by the traditional vampire vulnerability to water.
In spite of him becoming a vampire, DIO (JoJo's Bizarre Adventure) is immune to almost any weakness such as cross, he's only vulnerable to sunlight and Ripple/Hamon users.
Despite his former title as the world's weakest hunter, Sung Jin-Woo (Solo Leveling) was able break through the limitations of an average hunter after becoming a Player and the constant battles and training workouts within the System's quests.
Through centuries of dedicated training moving between both the Human and Underworld, Crom Cruach (Highschool DxD) transcended his limits, becoming stronger than, Ddraig, Albion, and powerful Gods using his basic skills, even overcoming the famed Dragon Slayers.
When he changes from alien to alien, Ultimate Ben (Ben 10: Ultimate Alien) is able to remove the physical vulnerabilities causes by the physiologies of certain alien species.
Thanks to the second skin provided by the Omnitrix, Ghostfreak (Ben 10) can venture out into the sun without harm.
As long as he abstained from drinking human blood, the Batman of Earth-43 (DC Comics) was immune to traditional vampire weaknesses, such as crosses and holy water.
Due to decades of exposure to Earth's Sun, Kal-El/Superman of the Kingdom Come universe (DC Comics) has developed an immunity to Kryptonite.
As a human-Kryptonian hybrid, Superboy (DC Comics) is more resistant to Kryptonite than pure-blood Kryptonians.
Being a clone created from the cells of countless of Kryptonians, H'El (DC Comics) is far more powerful than other Kryptonians, making him immune to Kryptonite and red sun radiation.
Having been created through a combination of Superman's DNA and Kryptonite, Superman X (Legion of Super-Heroes) is immune to Kryptonite.
AMAZO (DC Animated Universe) was able to transcend his limitations of his nanotechnology physiology by endlessly evolving.
As a "neo-vampire", Hannibal King (Marvel Comics) is resistant to sunlight and has only a craving for blood instead of an actual need for it.
As a dhampir, Eric Brooks/Blade (Marvel Comics) has all of the strengths and abilities of the vampire race with none of the weaknesses except for their thirst.
As a result of being experimented on by the Space Administration, the Venom symbiote (Marvel's Spider-Man) became desensitized to sonic attacks...
and evolved to be able to move and communicate without bonding to a host.
Vampirella (Vampirella) was born without any of the traditional vampire weaknesses, such as sunlight and holy objects.
Danny Fenton/Phantom (5 Years Later)
The Reapers (Blade II) are immune to all conventional vampire weaknesses except sunlight and heart destruction.
As the original Reaper, Jared Nomak (Blade II) has far better control over his blood-thirst and retains all of his higher brain functions.
Due to his advanced age and strength, Spike (Buffy the Vampire Slayer) is more resistant to sunlight and holy items than most vampires.
Due to his advanced age and strength, Angel (Buffy the Vampire Slayer) is more resistant to sunlight and holy items than most vampires.
Daniel "Oz" Osbourne (Buffy the Vampire Slayer) has been able to control his werewolf transformations through meditation and herbal remedies.
As a Lycan/vampire hybrid, Michael Corvin (Underworld) is immune to both species' trademark weaknesses.
Quint Lane (Underworld: Awakening) has incredible resistance to silver as a Lycan-Corvinus Strain hybrid, but a silver nitrate grenade going off inside his body was enough to kill him.
As a vampire/Corvinus Strain hybrid, Selene (Underworld) is unharmed by sunlight.
Katherine Pierce (The Vampire Diaries) has developed an immunity to vervain by repeatedly ingesting it in trace amounts.
Doomsday (DC Extended Universe)
After being implanted with the Mantra Reactor, Asura (Asura's Wrath) is able to freely channel his Wrath Mantra without fear of it backfiring and destroying his body.
As a dhampir, Rayne (BloodRayne) is immune to holy items and resistant to sunlight and water.
Kain (Legacy of Kain) has developed immunity to sunlight and certain forms of water (rain, snow, etc.)
Alex Mercer (Prototype) developed an immunity to the anti-Blacklight poison Bloodtox with repeated exposure.
The enhanced Type 2 Las Plagas (Resident Evil) were able to tolerate direct sunlight, though flash grenades were still fatal to them.
Rahab (Legacy of Kain: Soul Reaver) was able to overcome the vampire race's traditional vulnerability to water.
By consuming Rahab's soul, Raziel (Legacy of Kain) was able to overcome his vulnerability to water.
Daurgothoth, the creeping doom (Forgotten Realms) has transcended not only the limits of his undead body, but also the limits of the dragons species as a whole, developing new breath attacks that he shouldn't be able to use, as well as developing other abilities that should be impossible for him because of his undead status.
Dark Sister (Valkyrie Crusade) is a Vampire that is immune to all of an vampire's weaknesses, such as sunlight and holy powers and objects.
The Gem of Amara (Buffy the Vampire Slayer) renders any vampire who wears it immune to their conventional weaknesses, such as sunlight and stakes to the heart.
Superboy Prime (DC Comics) created a special powered suit, allowing him to maintain his powers even in the presence of a red sun.
Superman (DC animated universe) wearing a Kryptonite-proof suit.
When combined with the Stone Mask, the Red Stone of Aja (JoJo's Bizarre Adventure Part II Battle Tendency) allows a Pillar Man to overcome their vulnerability to sunlight & Hamon/Ripple.
When enchanted by witches and worn by vampires as jewelry, lapis lazuli gemstones (The Vampire Diaries) allow them to walk in daylight unharmed.
Gold Amazo finally meets Lex Luthor to destroy him - Justice League Unlimited
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