Pokémon Legends: Arceus might be laying the groundwork to establish the Pokémon Wars alluded to throughout Pokémon's sprawling history. For a long time, one of the prevailing theories surrounding Pokémon Red and Blue was that a Great Pokémon War took place shortly before the events of the game, which was further substantiated by Lt. Surge referencing how Pokémon saved his life during "the War." Furthermore, in Pokémon: Lucario and the Mystery of Mew, we see that Lucario fought during a very real, ancient war waged with Pokémon.
All of this indicates that Pokémon did fight in wars in the past multiple times across numerous continuities. However, Pokémon Legends: Arceus might very well allow audiences to partake in a Pokémon War that was waged centuries before modern Pokémon society in Sinnoh.
Pokémon Legends: Arceus appears to be drawing inspiration from Japan's Tokugawa Shogunate and Sengoku Period, often referred to as the Warring States period. This period of time was an over 150-year civil war between the various warlords and clans throughout Japan, led by samurai fighting for supremacy. Ultimately, three warlords ended up consolidating power during this era: Oda Nobunaga, Toyotomi Hideyoshi and Tokugawa Ieyasu. The war ended when Tokugawa Ieyasu overcame his rivals, leading Japan into the Tokugawa Shogunate.
Pokémon has actually incorporated this era into its lore already -- sort of. Pokémon Conquest is a crossover between the Pokémon franchise and the separate video game series Nobunaga's Ambition, which attempts to turn the Sengoku Period's wars into a fun strategy RPG. Pokémon Conquest takes place in the Ransei region, which indicates that the Warring States era is separate from Sinnoh and the like. However, the Ransei Region is said to have been created by Arceus, a fact further reinforced by how the island region resembles Arceus's silhouette.
Pokémon Conquest's canonicity is questioned in the context of the greater Pokémon universe. Mewtwo exists in the game, which is impossible, given that Mewtwo wasn't created until the modern era of Pokémon. However, what this establishes is that, in the prior generations of Pokémon, wars involving Pokémon took place and Arceus at some point stepped in to create territory where war could continue. Pokémon Legends: Arceus and Pokémon Conquest seem to occur in roughly the same era, and both place Arceus in an instrumental role.
What this shows is that Game Freak is willing to incorporate war into periods of Pokémon history inspired by real-world events -- or, at least, use Pokémon battles to establish different territory and objectives.
Then there's the question of Pokémon Legends: Arceus's villain team. Every Pokémon game has a villainous team of some sort, but recent games have taken steps to divorce themselves from the standard Team Rocket formula, introducing newer, more insidious villains. Pokémon Sun and Moon featured the Aether Foundation, while Pokémon Sword and Shield introduced players to Macro Cosmos. Both are more complex antagonist groups with more nuanced approaches to what they're doing, while Team Skull and Team Yell are more side-antagonists.
If Pokémon Legends: Arceus follows this trend, one can expect two antagonist teams: a group of bandits with their own short-sighted goals and a far larger threat. Potentially, a warlord fighting for supremacy in Sinnoh or someone hoping to use Arceus's powers of creation for ill-intent. This would fit in with the general structure of the last two generations of Pokémon games.
With that established, the events of the game might also be previously affected by an earlier war. Many people have compared Pokémon Legends: Arceus to The Legend of Zelda: Breath of the Wild, which takes place a century after a climactic war against Ganon. The game might very well be what people theorized Pokémon Red and Blue to be years prior: a nation recovering from a war that depopulated its cities.
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