DURING MAIN STORY:
Arceus-when you have all the castles, arceus will appear, you must link to it with the hero
AFTER:
Terrakion-Cragspur, have 70% link with bastiodon and it will appear. best link is keiji
Articuno- Nixtorm, clear mitsuhide's episodes, have all facilities at level 3 and it will appear. best link: mitsuhide
Registeel- Have 15+ warlords with best link and obtain Unifier crystal. will appear in valora, best link is leyasu.
Groudon- Terraria, clear shingens episode and have all facilities at level 3, best link is shingen
Dialga- valora, have rank 2 ina and tadakatsu, have the conquerer crystal, have 50+warriors. best link is tadakatsu
Mewtwo- illusio, clear kenshin's episode and have all facilities at level 3
Reshiram- Special event, best link hideyoshi
Zekrom- violight, have rank 2 nobunuga and warrior crystal. best link nobunuga
Rayquaza- Dragnor, have all other legendaries, best link nobunuga
SOURCE: http://www.serebii.net/conquest/legends.shtml
