Code Jack is available after meeting up with Arata after the prologue. You have to clear the field of at least half of the Field Bugs that are active (which is easy to do when the bugs are of decadence or magic, but not-so when they are of other types that can damage the characters heavily). Once this is done, press the Touch Pad to have Arata choose a command. From here, you can use Code Jack to influence to flow of combat, modify the genre of the battle, or even summon a previously felled Entoma Queen. Early on, your only Code Jack ability might be where you reload the field with magic bugs (which is a GREAT addition to use later on, as some field bugs are ridiculous or detrimental) so go ahead and use it to change the field and get the trophy.