Sho and Orochi can join you as allies under certain conditions. The exact conditions are unknown and may depend on the play number. If you want these characters as allies, play every battle against them and win. Make sure not to miss the Sho battle right before "Destroy the Flame Dragon"; to unlock it, win every battle up to that point. Also, some players claim that Sho will not join you if you take too much time to get through Story Mode.
--------------Hidden Story Mode Battles--------------
A number of Story Mode battles are easily missed because they only appear under certain conditions.
* Training battles involving Sho or Orochi will only appear if every character in the battle has joined you. There are several such battles.
* There are two versions of "The End of Death Commander Tama" in Greater Tricity Area. One version has a yellow icon and tends to appear in Play 1 if Orochi doesn't join you. The other version has a red icon. In the yellow version, you fight against Orochi and a Death Force team. In the red version, Orochi is absent. The yellow version gives you an opportunity to fight Victory Baron and Demon Wing. It is the only place where either of these borgs is guaranteed to appear.
* There are two versions of "Defeat a Death Commander" in the Construction Zone. In one version, you fight against Tama and a Death Force team. In another version, you fight against only Tama. These battles can appear if you lose certain battles involving the Death Crystals.
Some battles have the same names as other battles, so it's easy to mistakenly think you've played them.
* After you beat "Defeat the Elite Unit" at the Market Place, another battle with the same name appears at the same place. However, it is a totally different battle.
* After "The Gigantic Battle! Defeat the Cyber Death Dragon," a "Defeat the Death Force Unit" battle with a red icon appears at Stone River. This is not an ordinary Death Force unit battle; it contains Machine Head and Mechanical Dragon, and is the only battle that contains either of them. After you win, another battle with the same name and the same red icon appears at the same place. It is a different battle, though. It contains Death Head and Cyber Dragon.