After you conquered Ransei and returned the kingdoms to their Warlords, there was some talking in Valora. Ieyasu speaks eagerly on the peace of Ransei, thinking there is nothing left to desire.
Tadakatsu disagrees with him. He believes there is but one more thing left - Pokémon partners. Is that not a Warrior's goal: to be with friends with as many Pokémon as possible? Ieyasu decides to aim for one hundred Pokémon as his partner, then. And claims it reasonable.
So, how will THIS one work? You can pretty much just recruit Warriors and Link with Pokémon wherever you want. You have no need to conquer a kingdom, but it will be immensely helpful. Especially assuming you crazily go for all seventeen like you've done once or twice past, you can just spread Warriors across all the kingdoms and set most to delegate for searching.
Note: But, yeah, such a walkthrough here would be needless, pointless, and a waste of space. You know how to Link with Pokémon; you know how to locate them. The only thing walkthrough-worthy would be kingdom fights, but, as the previous story is, Warlords will invade each other and scramble everything up.
But, yes, you'll have to Link up with 100 Pokémon. This includes the Warriors in your army. So, in effect, you can just go ahead and Link during recruit battles or something. But, given the size of the menu markers, I'd say someone can only recruit up to six or eight Pokémon. You'll need to have 13 ~ 17 or more Warriors for that, which requires three or more kingdoms. So, yes, you will have to conquer a few kingdoms.
Initially, at the start, you'll want to conquer Nixtorm, then get some Ice Pokémon from there and beat up Dragnor and Avia. That'll get you started pretty well.
Again, recruit 100 Pokémon. All Pokémon owned across the army count. Good luck.