Team Warfare (Pokemon Mono and Sepia)

Team Warfare is an evil organization who plan to rid the world of ALL Pokemon! Led by the cruel and emotionless Atomar, they’ll stop at nothing even if it means siding with the enemy! They have a special man-made Pokemon named GPD-X, who have dark-magical attacks that can vaporize almost anything and anyone. And Team Warfare is using that kind of magic to commence Pokemon extinction! Only you can stop them and save the world!

Characters
Warfare Commander Brute is muscle of all of the organization. For a big strong man, he is clever and has a way with words.

Encounters
* Please note that battles listed here do not apply to Grunts and Leashers.

First Time (Stomping Grounds)
You'll first meet Team Warfare here (just one Grunt) and their over-the-top mission to rid the world of all Pokemon. Battle and defeat him, and he'll flee. A man who is victimized by him will reward you with a Great Ball after thanking you for saving his life.

Second Time (Warfare Post)
You'll stumble upon this little hideout at Nightmare Forest. After fighting two grunts (one male and one female), you'll be introduced to Commander Zoom, who then takes you on.

Third Time (Lorra Manor)
Sometime there, take on the female grunt. Before the banshee who haunts the place (not to mention she is the owner of this house) flees with three magical keys (meant to release Univamp, Unidoron, and Unigaru) so Team Warfare couldn't get them, you'll be confronted by the mysterious Oboe.

Fourth Time (Perilous Cave)
You'll eavesdrop on two grunts who were talking about the boss's uncouth relationship with the Capra Avenue gym leader Argos. After a moment, the two spot you and flee.

Fifth Time (Capra Academy)
While you and Wheeler are training at Capra Academy, you first meet Atomar. A while later, Team Warfare attacks the site. After battling a few grunts here and there, Atomar flees and orders Zoom to take care of you.

Sixth Time (Warfare Hideout)
After your errand at Kurosawe Boulevard, you'll be alerted that Team Warfare is wrecking havoc at Honda Bay. Before you go to their hideout located there, Oboe cuts your escape and challenges you to another battle.

Seventh Time (Toxic Swamp)
During your trek here to Dean Avenue, you'll come across Team Warfare up to no good as usual. Battle a couple of grunts and leashers here as you make your way out.

Eighth Time (Route 10; after winning the Smog Badge)
Sometime in the middle of this bit-of-a-complex trek through this route, Team Warfare is near. After you beat a couple of grunts, Zoom returns to attack you. Even without any Pokemon on his side, he isn't worried one bit. He is joined by two Warfare commanders Lust and Brute. And they have a secret weapon: the ability to become artificial Pokemon themselves! As Zoom, Lust, and Brute become cyborg Pokemon Cytora, Cynymph, and Cysaru respectively, you challenge them to a battle. (You really don't fight them like normal; this fight only happens in the cutscene.) They overwhelm and defeat you quickly, forcing you to find shelter at a kind old lady's rest house. After that, you continue your little war against Team Warfare. When you come back, you'll realize that they are destroying more and more Pokemon with GPD-Xs. When you confront Atomar once again, he is improving GPD-X too: by evolving it into APD-X! He shows you this creature's features, horrifying you in the process of how stronger than it is last time. He then orders Zoom, Lust, and Brute to destroy you as they change into their cyborg forms and you must have Round 2 with them, one at a time before you can take on Atomar.

Ninth Time (Carlson Labs)
Two Team Warfare grunts somehow have already broken in the lab so they can steal the formula to create an artificial evolutionary stone (Earth Stone), something that has to do with improving APD-Xs schematics even if it means evolving it into a more powerful Pokemon to release Chaovatar. Fight the two and they'll flee, even though they got the formula by taking pictures.

Tenth Time (Route 12)
While you make it through, battle a couple of grunts and leashers who are doing nothing but on a Pokemon-destroying mission. The leashers may have APD-Xs now, but they don't compare to Oboe as he confronts you yet again. After you beat him, Oboe accidentally drops a small photo of his deceased wife and son, and you pick it up. You were wondering why he joined Team Warfare. He angrily snatches it from you, and scolds you for getting into private affairs. You then question yourself: he wants to destroy all Pokemon...because they destroyed someone he cared for...? Later, he too questions himself as Warfare General, and starts to get more and more guilty of his actions against Pokemon.

Final Time Part 1 (Route 13)
After you win the Shadow Badge, Atomar makes a televised message, telling everyone that Chaovatar will come and destroy humanity unless everyone surrenders their Pokemon to Team Warfare. While panic ensues, you trek Route 13 on water while fighting several Trainers along the way, head to the island on the right, and confront Atomar here. He flees with a submarine back to headquarters. Fight a couple each of grunts and leashers before you dive and enter Warfare HQ.

Final Time Part 2 (Warfare HQ)
When you make it inside, feel free to explore every available room out there and battle any grunt and leasher in sight. Before you bust into Atomar's office, you spy on both him and Oboe. Atomar questions Oboe what is bothering him. Before he can answer, you barge right in to stop Atomar. You plead Oboe to understand that destroying Pokemon isn't going to bring his family back and only makes things worse. A grief-stricken Oboe is too angry to listen to you and battles you yet again. After you beat him, Oboe finally comes to a realization that what he has done only makes his pain and suffering the more painful. He then turns on Atomar, much to his dismay, and defects from the organization. Upset about this, he breaks his purifying pack that his mask was attached to. Thankfully, Oboe was able to rip all of this off since his illness was cured by that machine. Atomar flees to Hondo Bay as you and Oboe leave HQ and agree to work together to stop him. Oboe breaks out the news that Atomar's master plan is to release Chaovatar and take over the world. And his final specs on APD-X will be just a tool to commence Pokemon genocide! With help from Wheeler and Argos, head to Hondo Bay and dive into Kai-Mon Cavern for the final battle.

Final Time Part 3 (Kai-Mon Cavern)
By the moment you enter this cavern, you learn that releasing Chaovatar will also reawaken Kamijuu and Ojoniji, two godlike kaiju Pokemon that ravaged the Retoro Region with their series of fights centuries ago. Before you reach the very bottom, the Warfare Commander trio will face you one last time and more stronger than ever. Like last time, you'll fight them one at a time.

With XPD Infinite defeated, the crumbling Pokemon crashes down on Atomar's post, causing the Warfare Boss to leave Chaovatar's body. Before he can cowardly flee, remains of the dying XPD Infinite crush him to death. As a result, Team Warfare is no more.

After Oboe heals your Pokemon (he can do as many times as you like as long as Kamijuu/Ojoniji hasn't been battled or caught yet), Kamijuu/Ojoniji thanks you for your bravery, sees you as a worthy Trainer, and wants to fight you.

After Kamijuu/Ojoniji has been caught (defeating it causes this to reset until you got at least a second chance to capture that Pokemon), a sunset rises all over the Retoro Region, and now the whole world is at peace. Chaovatar now flees to parts unknown in peace (you'll fight and capture him at post-game.) Yet again you part ways with everyone after that fateful battle as you're on your way to your final challenge at Verley Hill Boulevard.

Trivia

 * Some point at Route 10, Warfare Commanders Zoom, Lust, and Brute were fused with Pokemon DNA, so in battle, they ARE the Pokemon. Zoom, Lust, and Brute become Cytora, Cynymph, and Cysaru respectively. After you defeat XPD Infinite and Atomar/Chaovatar and capture Kamijuu/Ojoniji, you can be able to catch Cytora, Cynymph, and Cysaru who are then spliced from their human forms just as Team Warfare disbands. They can be captured at Carlson Labs' reservation Tanner recently set up after.
 * The boss's name Atomar is a take on the German word "atomar", which is "atomic" in English.
 * Atomar has the same characteristics like Kurata Akihiro of Digimon: Data Squad and Harold Attinger from Transformers: Age of Extinction, who are willing to work with non-human species, despite their hatred for them, to get rid of those species.