Here's how it's supposed to work according to Games for Kids.
Object: To score more points each round than the opposing team (Ultimately to either capture the opposite teams flag or to kill their General).
Human Stratego Rules: This is a very fun but complex game. This game is a mixture of Capture the Flag and the board game Stratego. Each team has a set of different colored cards. These cards have varying amounts of different jobs (download an example here in MS Publisher). For numbers of cards see below. The teens run around with 1 and only 1 card from their team and can tag members of the opposite team. The weaker card surrenders its card to the more powerful card (higher point values win, a few exceptions apply). If the point values are the same, then they kill each other and both surrender their card to their opponent and both die. Each person keeps captured cards but they cannot be used (they are a different color). A dead person can go back to their team captain to obtain a new card. At any time a person may go to their team captain and exchange their card for another except the General who cannot change his card ever. The only card that is required to be in play is the General. The General is the most important person (and powerful) in the game. The General can kill everyone except the Assassin (who kills him) and the other General (which just walk away from each other). The Assassin works just like a regular card (kills based on point values) except in addition he can kill the General; however, there are only two of these and if they both die, the General cannot be killed. Another special card is the Bomb. The Bomb is only worth 50 points yet he kills everyone except the General and Bomb Squad, both of which kill the Bomb; however, the Bomb is passive and cannot tag anyone. If he is tagged, he kills whomever tagged them unless they are a Bomb Squad or General, in which case the Bomb dies. The Bomb Squad also works like a regular card (kills based on point value) except he can kill a bomb. Every other card (Marshall, Lieutenant, Captain, etc.) only kill based on point values.
Playing Human Stratego: Divide the teens into two even teams (both need athletic and smart teens). Each team needs 1 person to be a team captain (can be an adult helper or teenager). The team captain is responsible for assigning cards to individuals. Each team is given a certain area (part of a wooded area or building) and they are responsible for hiding their flag in this area. You choose how visible the flag should be (I recommend using Bandannas at least 1/4 part clearly visible). The flag cannot be continuously guarded and must be able to be easily accessed (Not up in a tree or out on a ledge of a building). Put team captains or other people in charge of making sure the flag is hidden in a legal area. Once everyone is ready, blow a whistle or something to let everyone know the game starts. Let them know that when the whistle blows again that the game is over. The round ends when (1) one of the Generals is killed, (2) one of the flags are discovered, or (3) 15 minutes of the game has passed. When the round ends have everyone come back to a central location. All Cards (their own and captured cards) are given to their team captain. Each team counts the value of the captured cards. Each team is awarded those points plus 750 if they captured the opposing team's flag (you can adjust as you please). Play 4 rounds (or as time sees fit) and announce final points at the end of all rounds.
Variations: You can add two cards later on in the later rounds. The first is the Atom Bomb. The Atom Bomb kills everything except the General (they both walk away). If they tag another Atom Bomb, they kill each other. The Atom Bomb can be used at the last 5 minutes of the 3rd and 4th round. The other card, the Hydrogen Bomb kills everything including the other General and the Atom Bomb. It is only killed by the other Hydrogen Bomb. It can be used at the last 2 minutes of the 4th round. You must explain their usage prior the start of the round you use them. Give them to the team captains and tell them they can be used when they blow their whistle 3 times. The players must swap their old card for the Atom or Hydrogen Bomb (Generals of course cannot swap).
Card Values and Amount:
# of Cards
Supplies: 2 flags (bandanas), 2 sets of cards in different colors, or 1 megaphone.
Downloads: Sam Lavender's rules and pieces in MS Publisher (here) 59 KB