-The Main Antagonist-

Darkrai:

Season 1's Saga #1 threat.
Darkrai used to be the Commander Of Team Debonair on season 1, he appears occasionally at certain episodes.
But on season 2, he makes his biggest role as the main antagonist. He is no longer a Team Debonair Commander as he quitted, he decides to take his revenge and kidnaps Team Megas's daughter, Kirlia. Darkrai has also been seen as an ally to certain villians and aids them to become stronger in order for them to take down Team Megas without too much effort. It is later revealed in special episode #8 that he is keeping Kirlia away from everyone because he feared the worst from Kirlia as he stated that Kirlia has the power to end the entire universe. He also never hurts Kirlia for whatever reason.

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-The Recurring Antagonist-

Abomasnow (Deceased):

Season 1's #2 threat. 
On season 1, Abomasnow is the second Commander Of Team Debonair, he is the biggest threat of all enemies that has ever costed.
But on season 2, Abomasnow is no longer the Commander of Team Debonair as he quitted, but was seeon again on the episode, "Scizor's icy love!" with a short debut where he wants his revenge on Team Megas but ultimately failed and was never seen again afterwards until Giratina Saga episode where he returned one last time for a fight. He became drastically stronger than before while gaining a new form in the process. He was able to take down the leaders of Team Megas, Team Pseudo and Team Heroes with ease. He was killed right after by Giratina himself when he blew up the earth and he was never revived ever again.

-The lord of Anti-Megas Alliance.-
-The bringer of earth's destruction. --
-The might of all evil-

Giratina (Deceased):


Season 2's #4 Saga threat.
Giratina is the mastermind behind the minds of Anti-Megas Alliance. He calm and composed no matter the situation he is in and he will not hesitate to take actions to cement whatever gap that needs to be sealed. Unlike any other villains, he takes it slow but steadily by accessing the situation first before coming up with the final plan. He is the final Saga threat and he is the first to blow up planet earth. Giratina can absorb his own fellow Scale Trio members, Palkia & Dialga to gain a new form. While he may be the minds behind the Anti-Megas Alliance, he is also the minds behind making this world all for his as he used all of his "allies" for them to do his dirty work to take out Team Megas but when they ultimately failed, he found no use for them anymore so he decide to kill them all along with Team Megas. He is the one responsible for killing Charizard. It is later revealed in special episode #8 that he is the one responsible for creating the Psycho Megas.

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-The Evil Version Of Team Megas-

 

Psycho Megas (Deceased):

Season 2's #1 Saga threat.
Psycho Megas are the evil version of Team Megas and is unknown where they came from. They are much stronger than Team Megas when they are all working together and only main weakness if Team Megas would battle one of their counterparts on a one on one battle. Psycho Megas soon slowly falls in defeat as Psycho Blaziken is the only one left but was granted by a power that Darkrai gave. Which is Dark Blaziken. Psycho Megas' only known appearence is on episode 47, Psycho Saga! It is later revealed in special episode #8 that Giratina is the one responsible for creating the Psycho Megas.

Dark Blaziken:

Dark Blaziken is Psycho Blaziken. The dark powers were given by Darkrai during the Psycho Saga to aid him in defeating Team Megas as he did not stood a chance and he was already fighting a losing battle. Dark Blaziken is extremely powerful, able to actually rival against Spirit Blaziken. However, he was eventually caught by Spirit Blaziken and he was absorbed by Blaziken and soon, Blaziken obtains the powers but he still has no control over it. His powers can only be unleashed if Blaziken is in an extremely dire situation and he is desperate to do something. Dark Blaziken is completely heartless and emotionless to anything that is good. He will kill anyone that he deems worthy of dying. He is pure evil and he will even go as far as hurting himself to satisfy his lust for blood.

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Team Go-Go!

Team Go-Go, another sinister team that collects powers from Pokemons for some purpose. They serve season two as the secondary antagonist. 
The supreme leader, Entei (Deceased):


The second in command, Tyranitar (Deceased):



Scizor (Female) (Deceased):



Season 2's #3 Saga threat.
It has been revealed that the mysterious Scizor from episode 35 is the member of Team Go-Go.

Slaking (Deceased):


Camerupt (Female) (Deceased):


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Team Go-Go's henchmen! 
Below is the list of henchmen for Team Go-Go as well as who they belong to. They are not real members of Team Go-Go but they are simply just hired to serve each respective members. It is unknown if Entei has a henchman or not yet.

Dusknoir & Magmortar (Camerupt) (Both deceased):



Trevenant (Slaking) (Deceased):


Delphox and Lucario (Scizor) (Both deceased):



Noivern (Tyranitar) (Deceased):


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-Other Villains-

The Deadly Of Everything!
Sinis Trio (All deceased):




Mismagius (Female) (Deceased):


Shiny Metagross (Deceased):


Team BlackHeart:



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Team Deboniar!

 

Team Debonair is season one's primary antagonist and they are an evil team capturing Pokemons, absord their powers to destroy earth. But soon Team Debonair was completely defeated by Team Megas and also by the help of other teams. The other remaining members quit Team Debonair but some left to go on to revive Team Debonair...

Team Deboniar Grunt:
Drapion:

Weavile:

Roserade:

Gliscor:

Spiritomb:

Yanmega

Honchkrow:


Team Deboniar Elite Grunts:
Magmortar

Rhyperior:

Salamence:

Tyranitar:

Torterra:

Dusknoir:

Aggron:


Team Deboniar Commanders:
Darkrai:
Info moved to above...

Abomasnow:
Info moved to above...

Team Deboniar Scale Trio:
Palkia, Dialga and Giratina (All deceased):

Giratina:
Info moved to above...

Palkia:


Dialga:


The Head Commander:
Rayquaza!


Season 1's #3 Saga threat.
Rayquaza is the head commander of Team Debonair. Rayquaza is a cold hearted and a very ruthless member in Team Debonair. He follows Blaziken wherever he goes till he felt like it's time to face them and ends up in an easy victory. He makes his biggest role in the episode "Rayquaza Saga!" as the main villian. Although cold hearted and ruthless, he is shown to be very loyal to his leader and even occasionally his fellow commanders. Rayquaza reappears in the final episode but met his bitter end after being defeated by our heroes and killed by Arceus for his selfish desire, Rayquaza is gone and never seen again... Or is it? 

And Now the Team Denoniar Big Boss, Arceus!!! (Deceased):

Arceus is the hidden main antagonist of season one and he makes his biggest role in Team Megas final episode and is the big boss of Team Debonair! But was defeated by Blaziken. It is unknown if Arceus survived or not, how he is evil and how he is the boss of Team Debonair. 


That's all, folks or is it...?