At the end of each stage you play through, you will face off against one or more giant sized pokemon with far more hit points than your pokemon and generally stronger attacks. You also face bosses and mini-bosses in the Battle Royale stages. You can also recruit the boss pokemon after a fight however this is not always possible. In addition, you fight against Zekrom at the beginning of the game and Cobalion (the first time) later on and neither of these fights you can win, they merely exist to further the story. To Find out about the Battle Royale bosses go to Battle Royale

Stage Boss 1 Boss 2 Boss 3 Boss 4 Boss 5 Boss 6 Boss 6
Beginning Garden Zekrom (undefeatable)
1-1 Trailhead Field Pignite (Meadow) Servine (Forest)
1-2 Seabreeze Trail Herdier (Meadow) Dewott (Beach)
1-3 Echo Valley Simisage (Forest) Simipour (Beach)

Simisear (Cave)

1-4 Challenger's Ground Zebstrika (Meadow) Liepard (Forest) Swanna (Beach) Gothorita (Tower)
2-1 Sun-dappled Bank Archen (Treetops) Tirtouga (Lake) Krookodile (Mysterious Fort)
2-2 Misty Edgewater Whimsicott (Forest) Swoobat (Cave) Lampent (Hauntyard) Garbodor (Filthy Fort)
2-3 Soothing Shores Scrafty (Tower) Stunfisk (Lake) Leavanny (Treetops) Bisharp (Greenleaf Fort)
2-4 Shimmering Lake Lilligant (Treetops) Seismitoad (Lake) Excadrill (Cave) Scolipede (Waterside Battlefield)
3-1 Rugged Flats Feraligatr (Beach) Sigilyph (Desert) Braviary (Canyon) Cofagrigus (Cave) Druddigon (Dragonbellow Fort)
3-2 Volcanic Slope Meganium (Autumnwood) Mandibuzz (Canyon) Darmanitan (Lava) Metagross (Foreboding Fort)

3-3 Firebreathing Mountain

Typhlosion (Lava) Galvantula (Factory) Sawsbuck (Autumnwood) Reuniculus (Tower) Gigalith (Mountain Path Battlefield) Zoroark (Cobalion's Castle)
4-1 Frozen Tundra Beartic (Glacier) Gothitelle (Tower) Escavalier (Cobalion's Fort 1) Accelgor (Cobalion's Fort 2)
4-2 Everspring Valley Venusaur (Forest) Stararaptor (Meadow) Blastiose (Lake) Gengar (Hauntyard) Charizard (Cave)
4-3 Sunny Sandshore Torterra (Desert) Machamp (Canyon) Empoleon (Beach) Infernape (Lava) Lucario (Factory)
4-4 World's Edge Hydreigon (Charge Battle) Haxorus (Team Battle) Cobalion (Team Battle)
World Pillar's Base 1 Serperior (Wood Area) Samurott (Beach Area) Emboar (Lava Area) Haxorus (Field Area 2) Chandelure (Shrine Area) Darkrai (Charge Battle) Giratina (Team Battle)
World PIllar's Base 2 Carracost (Swamp Area) Archeops (Wood Area 2) Klinklang (Production Area) Vanilluxe (Winter Area) Hydreigon (Tower Area) Volcarona (Cave Area) Reshiram (Charge Battle)
World PIllars Base Final Dark Rust (Final Area)

Stages without a boss have been excluded.