Originally Posted by Vulcan

There is a counter intelligence of some sort to go along with the spying? It would seem unruly to introduce an offensive only mechanic.

Generating more espionage points than your opponent will increase his espionage costs across the board and will also help catch enemy spies in your territory. A friendly spy can help protect a city or tile by doubling the cost of enemy missions in that tile. Once you get Democracy, you can build the Security Bureau building which will also help against enemy espionage missions. I don't see any way to stop the passive missions. Also keep in mind that this is the initial release and changes and tweaks may come with a patch.

Here's the Civilopedia entry for Espionage:

Espionage

Espionage Points

Using the Espionage Slider, players may assign a percentage of their trade income towards the production of Espionage Points. On the Espionage Screen, these points may be assigned to leaders that the player has met. These points may be used to perform various Active and Passive Espionage Missions. Active Missions require the player to spend Espionage Points and have a spy in the territory of the opponent they wish to perform the mission against. Passive Missions will take effect as the player accrues more points against a specific opponent. Having more espionage points accumulated will increase the cost of your opponents' missions towards you and reduce the cost of your missions towards them.

The Courthouse, Jail, Palace, Castle, Security Bureau and Intelligence Agency all increase the production of Espionage points. The Nationhood Civic also provides an Espionage bonus and the Security Bureau Building increases the point cost of enemy missions in your cities.

Espionage Screen

Espionage Points may be assigned to specific opponents on the Espionage Screen. If you do not assign points to specific leaders, they will be evenly divided between all known civs. By increasing the "Weight" item next to each opponent's portrait, you can assign the portion you would like each opponent to receive. Increasing the weight next to an opponent's name to "1" will assign all Espionage Points to that opponent. Increasing one opponent's weight to "2" while keeping two other opponents' weight at "1" and another's at "0" will give the first opponent twice as many points as the second and third, while the fourth will receive none. You may assign Weights in any fractions you like, up to 99. In this way, you can finely tune the portion of Espionage Points you would like assigned to each of your opponents. Below "Weight" is a number that shows the cost modifier for your Espionage Missions against this opponent. This number is based on the total number of Espionage Points you have spent throughout the game against this opponent. If the number is below 100% that means you have spent more on Espionage than your opponent, and your missions may be performed at a discount. If the number is greater than 100%, it means your opponent has spent more on Espionage than you. This will increase the cost of your Espionage Missions directed towards that opponent. The bottom item on the list states exactly how many Espionage Points you earn per turn towards that opponent. You can also see the Espionage Points you have against all players and the points they have against you by hovering the mouse over their score in the main interface. On the right half of the espionage screen is the list of all the Espionage Missions and their costs. You may click on an opponent's portrait to see a list of all their visible cities and the cost of missions in the selected city. Costs vary according to a number of factors, including the size of the city, its distance from your civilization, and religions present. If the cost of a Mission is blank, this means that the Mission requires more information to determine the exact cost, meaning you must move a spy into enemy territory before the mission cost can be determined.

Spies

Spies may be built by a Civilization that has researched The Alphabet. Spies differ greatly from most units. Completely invisible to enemy Civilizations, Spies can enter enemy territory to perform one Espionage Mission per turn. Active missions are tile sensitive, meaning you will have to sneak your Spy onto the enemy improvement or city you wish to affect. Performing a mission costs a certain number of Espionage Points and will cause an indicator to pop-up for your opponent over the location of the mission, informing him of the act (but not necessarily of your Spy). If the mission succeeds, the Spy may survive to perform more Missions, or she may be caught and destroyed. If the mission fails, the Spy will be destroyed, but no Espionage Points will be consumed. The cost of these Espionage Missions decrease the longer a Spy remains stationary on a tile, but every turn a Spy remains in enemy territory, there is a chance that she will be caught and destroyed. The chances of being caught increase with your opponent's Espionage spending, with the presence of a Security Bureau and if your Spy has recently performed a mission against that tile. If the Spy is caught, there is also a chance that its owner will be revealed. In addition to performing Espionage Missions, Spies also make excellent intelligence gatherers. They can use enemy roads and enter the cities of opponents with whom the player is at war, allowing the player access to otherwise unreachable information. The downside is that spies have a chance to get caught when they end their turn in unwelcome territory, even if they perform no active missions. Unwelcome territory is any territory belonging to a rival with whom you do not have an open borders agreement.

Missions

To perform an Espionage Mission, a player must move a Spy unit to the plot or city where they would like to perform the mission and select the Espionage Mission button. The Espionage Missions are:

Sabotage Improvement - Destroy an enemy improvement or route

Sabotage Building - Destroy a building within an enemy city

Steal Treasury - Steal a portion of your opponent's treasury, between 10 and 100%

Spread Culture - Increase your cultural influence in a city

Poison Water - Temporarily increase the amount of unhealthiness within an enemy city

Foment Unhappiness - Temporarily increase unhappiness within an enemy city

Support City Revolt - Send a city into revolt for one turn. This lowers enemy city defence, but does not remove cultural borders

Steal Technology - Steal a technology from an opponent

Sabotage Production - Destroys all hammers accumulated towards construction in a city

Sabotage Project - Destroys an already completed Spaceship Part

Influence Civics - Switch one opponent civic to match a civic you have adopted

Influence Religion - Switch an opponent's state religion to your state religion

Perform Counterespionage - Temporarily doubles cost of enemy espionage missions

Passive Missions

Passive Missions activate automatically as you accumulate certain levels of Espionage Points against an opponent. But as your opponent increases his own cache of Espionage Points, the Point costs of your Passive Missions increase in kind, requiring you to up your own Espionage spending to keep the effects. The Passive Missions are:

Can See Demographics - Allows you to see enemy demographics on the Info Screen [F9]

Can See Research - Allows you to see what your opponent is researching and how many turns they have until completion

City Visibility - Enemy cities are added to your visibility

Investigate City - You may enter enemy city screens by double-clicking on them

Spy Specialists

Spy specialists give a bonus to Espionage output and increase the chance of a Great Spy appearing in a city. The Courthouse, Jail, Intelligence Agency, Security Bureau, and Kremlin World Wonder allow the assignment of Spy specialists in a city.

Great Spies

Great Spies may occasionally appear in your city through the use of Spy specialists or Espionage-related Wonders. Invisible to all other units, Great Spies can explore rival territory, and will give a massive bonus of Espionage Points against a specific civilization if you expend the Spy in their city. They may also join a city as a super specialist, increasing science and espionage output of a city; or they may construct a Scotland Yard in a city, adding a significant bonus to Espionage production in that city.