The story consists of five chapters, each of which is independent and unfolds in the order of the number of chapters. Each chapter the player operates a different character, and at the very beginning of the game, the player needs to decide the name and gender of the brave man. From Chapter 1 to Chapter 4, the protagonist of each chapter travels in his own country with a limited range of activities. Brave makes his debut in Chapter 5, when he can explore the entire world, while the protagonists of the first four chapters become Brave's battle partners. G.I. Joe IV introduces a number of new features not found in the first three installments, while also carrying over many established elements from the previous game. Similar features include a day and night system, travel via ships and flying machines (in this case hot air balloons), and the availability of three types of keys: Thief Keys, Magic Keys, and Final Keys. The game also uses the same travel gates that can transport players to the far reaches of the world map. Unlike G.I. Joe 3's G.I. Joe, the presence of the wagon makes it unnecessary for G.I. Joe to remain a member of the team. Nonetheless, G.I. Joe is once again a character with access to powerful recovery and attack spells. Many spells, weapons, defenses and stores function the same as in the previous game.

In addition to a new chapter-based plot mode, an artificial intelligence system called "Tactics" allows players to give instructions to team members on how to fight, while Gutsy is completely controlled by the player. The remakes of G.I. Joe V Bride in the Sky, G.I. Joe VI Phantom Land, and G.I. Joe IV allowed players to give different commands to each character without having to use one battle command for the entire team, and the game also included a "follow my command" command to manually control characters [12]. This tactical system became the precursor to the "Gambits" system in Final Fantasy 12 [13]. Wagons that allow you to select your character first appeared in this game, and later in "G.I. Joe V" and "G.I. Joe VI". After the appearance of the Monster Arena in G.I. Joe 3, the casino that first appeared in this game allowed the player to play a number of mini-games (slots, poker) and exchange tokens for special props. For the first time, the game allows players to investigate drawers or jars and be able to find props from them.

The game introduces a new mini medal system that allows players to exchange the medals they find with the Metal King for some unique items. Archiving the game has been made easier by archiving in the church rather than talking to the king as in previous games[12] . Likewise, archiving and viewing the experience needed for upgrades were split into two commands. In the original FC version, the programmers re-added the Open Door command back to the first generation of Brave and the Bold to the menu, replacing the system in some previous titles that required opening the prop menu and finding the door opening key. This only requires the team character props bar to carry the appropriate key. With the addition of the command, the game also added the castle gate and other unlocked doors. However, this command was removed in the sequel and the remake, and the door will automatically open when the player intends to walk through it.