Types and Contexts of Combat

There are two major contexts in which combat occurs in PTU, and believe it or not, this is actually very important to how you treat combat mechanics and the way certain parts of combat work.
The first major context is, of course, in League-sanctioned Pokémon battles or casual battles that follow League rules and regulations. In such battles, it is usually not kosher for Trainers to directly interfere, such as by attacking their opponent’s Pokémon or using supernatural powers to influence the tide of battle. See page 440 for guidelines on League Legality.
The other major context comprises all other “full contact” fights where League rules and regulations don’t apply, including encounters with wild Pokémon, fights against unscrupulous criminals, and other battles in which Trainers would directly participate and even be targets of attack.
Both Initiative and Switching Pokemon work slightly differently depending on the type of combat in order to reflect the Trainer’s differing role in the conflict. Switching Pokémon is slightly more difficult in League Battles to prevent Trainers from simply switching all the time in an official match to gain advantage, for example. Both types of combat are likely to show up in most campaign types, and GMs should be careful to warn players if one type of combat will be much more prevalent than the other.
For example, in an average Pokémon campaign, the Ace Trainers and Commanders will have their chance to shine in Gym Challenges and tournaments, but Martial Artists will be better able to stand their ground when a criminal Team attacks or when wild Pokémon are rampaging. However, in a region in which there’s very little criminal activity and even the wild Pokémon are relatively tame, Trainers specializing in full contact fights won’t feel as useful.
In each round of combat, players get to take two turns: one for their Trainer, and one for a Pokémon. Even if their Trainer is knocked out or incapacitated, they still get their Pokémon’s turn and vice versa.
Additional Trainer Pokemon on the field that do not receive actions in a round can still be targeted by attacks and are treated as if unable to take actions that round for effects like Poison and Burn.