Place your Agents on assignment by sending them to an enemy City from the Covert Operations screen. Avoid assigning anyone against colonies that you need to keep friendly; you're always going to be taking a risk when you launch Operations against your opponents. It's best to be aware of this and to work against people who are already enemies or other dangerous opponents.
Give your Agents a few turns to travel to their new location, and then give them Operations to attempt against the target City.
Covert Operations
|
Assignment |
Difficulty |
Requirements |
Effect |
|---|---|---|---|
|
Establish Network |
Very easy |
None |
Gather information about the city, the network remains until the Agent leaves the city or is killed; very low risk, great when assessing territory for attack |
|
Siphon Energy |
Easy |
None |
Steals Energy from the City; this does not actually reduce the reserves in your rival's stockpile |
|
Steal Science |
Easy |
1 Intrigue |
Steals Science from the City; this does not actually reduce your rival's Science output |
|
Steal Technology |
Moderate |
2 Intrigue |
Steal a random technology |
|
Recruit Defectors |
Moderate |
3 Intrigue |
Recruit a random military unit which will be placed near your Capital |
|
Hack Satellites |
Moderate |
4 Intrigue |
De-orbit satellites within 5 hexes of the City |
|
Coup D'etat |
Moderate |
5 Intrigue |
Claim control of the City for yourself |
|
Dirty Bomb |
Hard |
5 Intrigue, 11 Purity |
Detonate a nuclear device in the city, reducing the City's population by half |
|
Call Worm Strike |
Hard |
5 Intrigue, 11 Harmony |
Activate a harmonic device that attracts Siege Worms to a City (Chomp!) |
|
Sabotage |
Hard |
5 Intrigue, 11 Supremacy |
Pillage all improvements within 3 tiles of the City |

The higher the difficulty, the better the chance that your Agent won't be able to complete the assignment. However, there are different tiers of failure. Success is rather direct; you get what you wanted out of the Operation. Failure is a sliding scale, where the penalties might be anything from minor to severe.
Operation Outcomes
- Undetected: The defending player is not notified that anything has happened (whew!).
- Detected: The defending player is notified that a Covert Operation took place, but not told who perpetrated it.
- Identified: The defending player is notified that a Covert Operation took place and told who perpetrated it. The Agent survives, but you face diplomatic complications.
- Killed: The defending player is notified that a Covert Operation took place and told who perpetrated it; your Agent is killed, and you face diplomatic complications.

To maximize your chance of success and to avoid diplomatic issues, only send your more experienced Agents to do dangerous tasks. Have people "train" by working on establishing networks and stealing Energy and Science. These tasks aren't as difficult or as dangerous, so you can get your Agents to higher ranks somewhat safely.
When attempting really tough Operations, have your best Agent go to the target City, and have other Agents return to Headquarters while using Operations Reconnaissance as your National Security Project. That gives you the best chance to succeed in your endeavor.
Spies start as Recruits, level into Agents, and then become Special Agents. Higher-tier Agents not only succeed more often, but they also obtain better results. They'll gain more information when establishing networks, steal more Science and Energy for your colony, and look suave while doing it all. The difference between spy ranks is very substantial. Secret Agents, for example, steal roughly triple the amount that Recruits gain.
Safe Spying
Figure out a style of spying that works best for your colony. It's easy to sit back and defend the entire game because that's safe. It's simple. But, it's also a massive waste of your potential. Careful spying gets you a huge boost to your yields and doesn't have to tick off the entire world. There are ways to avoid consequences while spying.

First, try targeting just one rival. If you spy against everyone and have a string of failures, you might get into a rather ugly war. If you're not ready to take on the world, pick your worst enemy, and send all of your Agents into their Cities. Even if they fail, you aren't getting into any new trouble because things were already sour with that rival.
Another option is to stay modest with your goals. Stealing Energy and Science isn't going to backfire too often. Don't try to reach beyond these easy tasks, and enjoy a long game of free income.
Tactical Observation
Stealing is all well and good, but Agents can also help you win wars. If you're looking for a weak spot in your opponent's border, go beyond scouting. Send Agents into border Cities, and establish networks there. Use this to look into enemy troop dispositions, the lay of the land, and the purpose of your enemy's city. What are they doing there? Can the city be approached easily from a side that you couldn't see before?
Establishing open borders serves a similar function, but that can be costly and is hard to set up with nations that you're planning to attack. Why pay for your scouts to walk through when your Agents can travel free of charge? Hey, it's only taxpayer money, right?

Covert Domination
Use Coups to take out enemy Capitals if they're foolish enough not to protect their best Cities. It won't matter if you can't keep the Capital beyond those early turns; the point is to ruin another person's chance at a Domination victory. This is nice if you're trying to win via Domination, or if you're afraid that another player is going to try to take over the world. Take that opportunity away, and you might force them into trying a more peaceful route. Even if they regain their City, you've succeeded in seriously hindering their progress for quite some time.