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Description
This basically details the exact layout of the way I handled the Legendary Pokemon in my Nuzlocke series. For exact term specifics:

-House Master: Whoever currently leads the Legendaries. In Gen I to IV, this is solely Arceus, but at the end of Diamond Nuzlocke when Arceus is killed, this title is inherited by Kyurem by default, because it's two formes have the next highest Base Stat Total at 700 (Compared to Arceus's 720 and Mewtwo and several others' 680). In terms of protagonists to inherit this title. The name House Master is when Kyurem takes over, as it's simply called Alpha during Arceus's reign.
-House Gate: BST 680 Legendaries. Palkia would've been included, but Palkia is deceased in the storyline for specific reasons not revealed yet, so this title is held by Mewtwo, Lugia, Ho-Oh, Rayquaza, Dialga, and Giratina. These are basically the gates that prevent Arceus from being targeted so long as they live.
-Alternate Gate: Legendaries that are too powerful to be considered normal Gates. This applies to Latias, Latios, Heatran, Regigigas, Cresselia, Darkrai, and Shaymin.
-Gatekeepers: Pseudo-Legendaries. Dragonite, Tyranitar, Metagross, Garchomp, Hydreigon, and Volcarona fill in this role. Salamence is also a Pseudo-Legendary, yet isn't a Gatekeeper, because it gave the title to Metagross instead because it was more capable of controlling the Golems. However, if I had actually caught Salamence, it WOULD have been a Gatekeeper; I simply took the easy way out with the free Metagross from Steven. Volcarona is included but isn't a Psuedo-Legendary, all because there happen to be two trios of Gates in Unova rather than one like the previous regions, and since Volcarona was the closest thing to a second Pseudo-Legendary it was given the role by default.
-Gates: The lowest classes of Legendaries. Weaker than the Gatekeepers, they are usually controlled, killed, or captured solely by their Gate Keepers, though the Golems can also be controlled by Regigigas. If a Gate is encountered before a Gatekeeper is present, typically the closest link to the Gatekeeper will give another Pokemon temporary control over how to deal with the gates, as the case of Rosa and Yosemite as they both caught Raikou and Entei respectively, and stopped when Argentino rightfully took over his own role to catch Suicune.

Storyline:

35 years ago, a group of five lead to the creation of Mewtwo, the first House Gate of the Alpha Legion. At this time, Arceus was not evil, and there was nothing but peace. However, it became prophesied that from these five humans, the creation of an "Omega" that will destroy Arceus caused him to change the entire universe into a hell whole before such a being could arise. Mewtwo, having essentially been a give-away to Arceus's plans, was sealed away by Lugia using the Kanto Gates, Articuno, Zapdos, and Moltres. Because of the Nuzlocke rules that Arceus set, and the fact only a Dragonite could unseal the gates to Mewtwo, Arceus figured his plans would be unchallenged.

16 years later, Marty arrives onto the scene with his own team of Pokemon, each team always beginning with a Water Type Starter Pokemon, with Marty himself based off the Guardian Beast Tyrannosaurus of Zyuranger, Arceus believed this was the Omega that was long foretold, but chose not to appear and let Marty's actions decide that answer for him. This eventually proved to be the case, as Marty obtained Dratini via the Game Corner, and without much difficulty trained it to Dragonite, which completely baffled Lugia and Arceus that a Gatekeeper would've actually been obtained in a Nuzlocke, especially one of Dragonite's Evolution Requirement being the highest. Kanto was then swiftly cleared out, the Kanto Gates killed, and Mewtwo released and joining Marty's team, which severely pissed off Lugia.

3 years later, Marty re-appears as Mythical Chi Beast RyuuseiOh but with no memories, and yet again begins his team through Johto. Because Larvitar was only obtained at Mt. Silver, Arceus severely doubted he'd be in much danger; He was wrong, as Marty got lucky by chance and obtained Larvitar and got it up to Tyranitar almost as quickly as he had faced Red. Little did they know Larvitar's capture was all thanks to the mysterious Mighty, a Charizard with a bit of history with Marty, but is rarely seen anymore. Even then, even without Argentino, they would've caught the Beasts anyways because prior to Argentino's evolution to Tyranitar, they already caught Raikou and Entei, and needed merely Suicune, which they obtained almost right away thanks to Argentino. With the three beasts caught, Ho-Oh is then caught and agrees to Marty's terms of reviving Shout, all because of how fierce Argentino is. At the end of this season, Shout is revived and the three beasts and Ho-Oh perish, as Arceus begins to take more direct actions.

Seeing Marty is becoming a legitimate threat now, Arceus gives Latios the order to capture a female Gardevoir whose name is unknown to help him construct his own Mecha to counteract Marty, who appears as Power Animal GaoLion now, and, of course, creates a team of Pokemon with a Water Starter. This backfires due to extra-universal interference from another universe's Giratina, which had Giratina not caused the plan to begin too early, they would've destroyed Marty. With the GaoHunter mecha destroyed, and V-Rex setting off to aide Marty's quest by clearing out Orre, Arceus sends Kyogre to revive and brainwash three of Marty's deceased Pokemon to use in his plans, but this does not go well for the same reasons, as James' Focus Punch causes Kyogre to forget what he was supposed to do next with these three and thus both he and the three Pokemon were killed for the final time. Rayquaza, not wanting any stupidity, brings in Latios to deal with Marty, but apparently the very reasons for Latios' high status all rely in his deal with Satan, which ultimately causes the deaths of Latias and Latios, and eventually a final confrontation with James leading to Rayquaza's death. Enraged, Arceus reveals his true colors knowing the fact that Kanto, Johto, and Hoenn were mere warm-ups compared to the power of the remaining Alpha Legion in Sinnoh.....

Old Alpha Legion:
Arceus
-Mewtwo
-Dragonite
-Articuno
-Zapdos
-Moltres
-Lugia
-Ho-Oh
-Tyranitar
-Raikou
-Entei
-Suicune
-Rayquaza
-Kyogre
-Latias
-Latios
-Metagross
-Regirock
-Regice
-Registeel
-Dialga
-Garchomp
-Uxie
-Mesprit
-Azelf
-Heatran
-Rotom (Yes I know it's not a Legendary, but there's a reason it's involved in the Legion)
-Regigigas
-Cresselia
-Giratina
-Darkrai
-Shaymin

Neo Alpha Legion (Post Arceus)(Not Pictured):
Kyurem
-Victini
-Reshiram
-Volcarona
-Tornadus
-Thundurus
-Landorus
-Zekrom
-Hydreigon
-Cobalion
-Terrakion
-Virizion

Unknown Affiliation (Post Kyurem)(Not Pictured):
-Xerneas
-Yveltal
-Other Gen VI Legendaries and or Pseudo-Legendaries

Not Mentioned (Non-Pokemon/Fakemon):
-Marty
-Zerosus
-Ghost Raptor
-????? ?????
-???????
-????????

Sprites Credits:
-Pokemon Red/Blue
-Pokemon Gold
-Pokemon Ruby/Sapphire
-Pokemon Diamond/Pearl

Titles for Trivia Purposes:
Arceus: Aurea sed ira Dei (Latin for Golden God's Wrath)
-Mewtwo: Judge of Genesis
-Dragonite: Great God Dragon
-Articuno: First Jury
-Zapdos: Second Jury
-Moltres: Third Jury
-Lugia: Silver Warden
-Ho-Oh: Eternal Gold
-Tyranitar: Imposing Force
-Raikou: Swift Thunder
-Entei: Blazing Inferno
-Suicune: Calming Rain
-Kyogre: Rain of Life
-Latias: Sorrowful Sister
-Latios: Bastard Brother
-Rayquaza: Highest Point
-Metagross: Ace of Aces
-Regirock: Petrae
-Regice: Glacies
-Registeel: Ferro
-Dialga: Doctor
-Garchomp: Draco irae (Latin for Dragon's Wrath)
-Uxie: Soothing Mind
-Mesprit: Soothing Emotions
-Azelf: Soothing Will
-Heatran: Hidden Potential
-Rotom: Fake Decoy
-Regigigas: Ingentes (Latin for Giant)
-Cresselia: Last Dream
-Giratina: Queen Abomination
-Darkrai: First Nightmare
-Shaymin: Tortured Sleeper

Kyurem: Aftermath Takeover
-Victini: First Test
-Reshiram: Yang of Fire
-Volcarona: Solar Deity
-Tornadus: Storming Fujin
-Thundurus: Blitz Raijin
-Landorus: Panther Inari
-Zekrom: Yin of Thunder
-Hydreigon: Moon Deity
-Cobalion: Athos
-Terrakion: Porthos
-Virizion: Aramis

-Xerneas: Absolute Life
-Yveltal: Absolute Death

Marty: Omega Red
-Zerosus: Satan's Punishment
-Ghost Raptor: Spirit of Ice
-????? ?????: Known by the same name as another
-???????: Final Enemy
-????????: I am the Alpha and the Omega

Description
This basically details the exact layout of the way I handled the Legendary Pokemon in my Nuzlocke series. For exact term specifics:

-House Master: Whoever currently leads the Legendaries. In Gen I to IV, this is solely Arceus, but at the end of Diamond Nuzlocke when Arceus is killed, this title is inherited by Kyurem by default, because it's two formes have the next highest Base Stat Total at 700 (Compared to Arceus's 720 and Mewtwo and several others' 680). In terms of protagonists to inherit this title. The name House Master is when Kyurem takes over, as it's simply called Alpha during Arceus's reign.
-House Gate: BST 680 Legendaries. Palkia would've been included, but Palkia is deceased in the storyline for specific reasons not revealed yet, so this title is held by Mewtwo, Lugia, Ho-Oh, Rayquaza, Dialga, and Giratina. These are basically the gates that prevent Arceus from being targeted so long as they live.
-Alternate Gate: Legendaries that are too powerful to be considered normal Gates. This applies to Latias, Latios, Heatran, Regigigas, Cresselia, Darkrai, and Shaymin.
-Gatekeepers: Pseudo-Legendaries. Dragonite, Tyranitar, Metagross, Garchomp, Hydreigon, and Volcarona fill in this role. Salamence is also a Pseudo-Legendary, yet isn't a Gatekeeper, because it gave the title to Metagross instead because it was more capable of controlling the Golems. However, if I had actually caught Salamence, it WOULD have been a Gatekeeper; I simply took the easy way out with the free Metagross from Steven. Volcarona is included but isn't a Psuedo-Legendary, all because there happen to be two trios of Gates in Unova rather than one like the previous regions, and since Volcarona was the closest thing to a second Pseudo-Legendary it was given the role by default.
-Gates: The lowest classes of Legendaries. Weaker than the Gatekeepers, they are usually controlled, killed, or captured solely by their Gate Keepers, though the Golems can also be controlled by Regigigas. If a Gate is encountered before a Gatekeeper is present, typically the closest link to the Gatekeeper will give another Pokemon temporary control over how to deal with the gates, as the case of Rosa and Yosemite as they both caught Raikou and Entei respectively, and stopped when Argentino rightfully took over his own role to catch Suicune.

Storyline:

35 years ago, a group of five lead to the creation of Mewtwo, the first House Gate of the Alpha Legion. At this time, Arceus was not evil, and there was nothing but peace. However, it became prophesied that from these five humans, the creation of an "Omega" that will destroy Arceus caused him to change the entire universe into a hell whole before such a being could arise. Mewtwo, having essentially been a give-away to Arceus's plans, was sealed away by Lugia using the Kanto Gates, Articuno, Zapdos, and Moltres. Because of the Nuzlocke rules that Arceus set, and the fact only a Dragonite could unseal the gates to Mewtwo, Arceus figured his plans would be unchallenged.

16 years later, Marty arrives onto the scene with his own team of Pokemon, each team always beginning with a Water Type Starter Pokemon, with Marty himself based off the Guardian Beast Tyrannosaurus of Zyuranger, Arceus believed this was the Omega that was long foretold, but chose not to appear and let Marty's actions decide that answer for him. This eventually proved to be the case, as Marty obtained Dratini via the Game Corner, and without much difficulty trained it to Dragonite, which completely baffled Lugia and Arceus that a Gatekeeper would've actually been obtained in a Nuzlocke, especially one of Dragonite's Evolution Requirement being the highest. Kanto was then swiftly cleared out, the Kanto Gates killed, and Mewtwo released and joining Marty's team, which severely pissed off Lugia.

3 years later, Marty re-appears as Mythical Chi Beast RyuuseiOh but with no memories, and yet again begins his team through Johto. Because Larvitar was only obtained at Mt. Silver, Arceus severely doubted he'd be in much danger; He was wrong, as Marty got lucky by chance and obtained Larvitar and got it up to Tyranitar almost as quickly as he had faced Red. Little did they know Larvitar's capture was all thanks to the mysterious Mighty, a Charizard with a bit of history with Marty, but is rarely seen anymore. Even then, even without Argentino, they would've caught the Beasts anyways because prior to Argentino's evolution to Tyranitar, they already caught Raikou and Entei, and needed merely Suicune, which they obtained almost right away thanks to Argentino. With the three beasts caught, Ho-Oh is then caught and agrees to Marty's terms of reviving Shout, all because of how fierce Argentino is. At the end of this season, Shout is revived and the three beasts and Ho-Oh perish, as Arceus begins to take more direct actions.

Seeing Marty is becoming a legitimate threat now, Arceus gives Latios the order to capture a female Gardevoir whose name is unknown to help him construct his own Mecha to counteract Marty, who appears as Power Animal GaoLion now, and, of course, creates a team of Pokemon with a Water Starter. This backfires due to extra-universal interference from another universe's Giratina, which had Giratina not caused the plan to begin too early, they would've destroyed Marty. With the GaoHunter mecha destroyed, and V-Rex setting off to aide Marty's quest by clearing out Orre, Arceus sends Kyogre to revive and brainwash three of Marty's deceased Pokemon to use in his plans, but this does not go well for the same reasons, as James' Focus Punch causes Kyogre to forget what he was supposed to do next with these three and thus both he and the three Pokemon were killed for the final time. Rayquaza, not wanting any stupidity, brings in Latios to deal with Marty, but apparently the very reasons for Latios' high status all rely in his deal with Satan, which ultimately causes the deaths of Latias and Latios, and eventually a final confrontation with James leading to Rayquaza's death. Enraged, Arceus reveals his true colors knowing the fact that Kanto, Johto, and Hoenn were mere warm-ups compared to the power of the remaining Alpha Legion in Sinnoh.....

Old Alpha Legion:
Arceus
-Mewtwo
-Dragonite
-Articuno
-Zapdos
-Moltres
-Lugia
-Ho-Oh
-Tyranitar
-Raikou
-Entei
-Suicune
-Rayquaza
-Kyogre
-Latias
-Latios
-Metagross
-Regirock
-Regice
-Registeel
-Dialga
-Garchomp
-Uxie
-Mesprit
-Azelf
-Heatran
-Rotom (Yes I know it's not a Legendary, but there's a reason it's involved in the Legion)
-Regigigas
-Cresselia
-Giratina
-Darkrai
-Shaymin

Neo Alpha Legion (Post Arceus)(Not Pictured):
Kyurem
-Victini
-Reshiram
-Volcarona
-Tornadus
-Thundurus
-Landorus
-Zekrom
-Hydreigon
-Cobalion
-Terrakion
-Virizion

Unknown Affiliation (Post Kyurem)(Not Pictured):
-Xerneas
-Yveltal
-Other Gen VI Legendaries and or Pseudo-Legendaries

Not Mentioned (Non-Pokemon/Fakemon):
-Marty
-Zerosus
-Ghost Raptor
-????? ?????
-???????
-????????

Sprites Credits:
-Pokemon Red/Blue
-Pokemon Gold
-Pokemon Ruby/Sapphire
-Pokemon Diamond/Pearl

Titles for Trivia Purposes:
Arceus: Aurea sed ira Dei (Latin for Golden God's Wrath)
-Mewtwo: Judge of Genesis
-Dragonite: Great God Dragon
-Articuno: First Jury
-Zapdos: Second Jury
-Moltres: Third Jury
-Lugia: Silver Warden
-Ho-Oh: Eternal Gold
-Tyranitar: Imposing Force
-Raikou: Swift Thunder
-Entei: Blazing Inferno
-Suicune: Calming Rain
-Kyogre: Rain of Life
-Latias: Sorrowful Sister
-Latios: Bastard Brother
-Rayquaza: Highest Point
-Metagross: Ace of Aces
-Regirock: Petrae
-Regice: Glacies
-Registeel: Ferro
-Dialga: Doctor
-Garchomp: Draco irae (Latin for Dragon's Wrath)
-Uxie: Soothing Mind
-Mesprit: Soothing Emotions
-Azelf: Soothing Will
-Heatran: Hidden Potential
-Rotom: Fake Decoy
-Regigigas: Ingentes (Latin for Giant)
-Cresselia: Last Dream
-Giratina: Queen Abomination
-Darkrai: First Nightmare
-Shaymin: Tortured Sleeper

Kyurem: Aftermath Takeover
-Victini: First Test
-Reshiram: Yang of Fire
-Volcarona: Solar Deity
-Tornadus: Storming Fujin
-Thundurus: Blitz Raijin
-Landorus: Panther Inari
-Zekrom: Yin of Thunder
-Hydreigon: Moon Deity
-Cobalion: Athos
-Terrakion: Porthos
-Virizion: Aramis

-Xerneas: Absolute Life
-Yveltal: Absolute Death

Marty: Omega Red
-Zerosus: Satan's Punishment
-Ghost Raptor: Spirit of Ice
-????? ?????: Known by the same name as another
-???????: Final Enemy
-????????: I am the Alpha and the Omega