Secret Agent consists of 3 episodes in the DOS version, with Secret Agent HD adding a 4th. Though installed separately in the original, the HD version has all of them accessible from the same title menu.
The first three episodes all feature the same set of elements and not much in the way of a story, so they can technically be played in any order. However, as the average stage difficulty does increase somewhat, playing them in the intended order would make the most sense.
- The Hunt for Red Rock Rover (free Shareware episode)
- Kill Again Island
- Dr. No Body
The new episode added by the HD version contains a number of new enemies and objects, notably the Jetpack and Scuba Gear, and is also considerably harder than the original game. Though it can also be played at any time, attempting it without having at least some familiarity with the game is not recommended.