Now you need to choose between Terrera or Illusio, You only need to beat one of them. This guide based on Terrera.
I choose Terrera because:
 Their Pokemon consists of fire and ground type, which is very easy to dealt with water POkemon. There are many Water Pokemon you can catch on Fontaine.
 Illusio has psychic type, they’re weak to bug pokemon, which is quite annoying because bug Pokemon are generally weak at this moment (sewaddle…)
Even with all those things, Terrera is still a little bit hard. However you can cheat a little by using Pokemon’s password to obtain gyarados (mq2xRVNgRL).
Use the password from the menu and then you’ll be informed that gyarados has appeared on certain town. Save your game and try to capture it with the person who has gold link on their hand to get the best link (it’s important because gyarados is a strong Pokemon that you’re probably gonna use until you beat this game).
If you feel that using a password is cheating then I suggest you to catch magikarp (Fontaine) and then train it until it evolves to gyarados (you can also use panpour, etc). Train your army until you reach about 1200-1300 strength and then attack Terrera.
Tips: Gather all your squad member at Pugilis
Event, unfortunately you can’t challenge him yet. You’ll go back to Pugilis and will be attack by Yukimura (Shingen’s army minus himself). The battle is very easy, since the majority of them are fire Pokemon and you’re fighting on Pugilis. Use the same tactic as before (knock them out from the gambling area).
Your warrior will evolve after this battle and you can challenge Shingen now. Advance to the next month (since you can’t attack Shingen at this moment).
Attack Shingen now,
|Rhyperior||Ground/Rock||Rock Wrecker||Lightning rod|
|Scraggy||Dark/Fight||Faint Attack||Shed Skin|
You don’t need to defeat all enemies, simply capture 3 flags and you’ll win. However there is aw ind that will blow you down every 2-3 turns and deals ground damage to your Pokemon. It’s very easy to do since Shingen’s Pokémon have a small moving range.
Capture one flags to be safe, and then you can let him climb the tower and wait till the wind blows his Pokemon, it’ll deal about 30-40 damage if it’s fire type but very little to ground type Pokémon. I simply kill all his Pokémon using my gyarados .
After the battle Kenshin will also automatically join your party. Now you get 2 strong Pokémon with perfect links (Gallade and Rhyperior).