Skorpios
Chieftain
Hopefully, CivBE's espionage system will be the topic of a Firaxis livestream before release, but until then let's throw around some speculations on what we know and what we'd like to see.
So far we've snatched glimpses of early, low-level Covert Ops and the Affinity-locked missions:
Establish Network
Siphon Energy
Steal Science
Steal Technology
Dirty Bomb (Purity)
Worm Strike (Harmony)
Sabotage Mission (Supremacy)
The image above also shows a 'At Headquarters' section with:
"National Security Project: Propaganda - +1%(?) Health for each agent at Headquarters" with a button marked 'Switch Project'.
This suggests that your agents can be assigned to the National Security Project to affect your entire colony in various ways. Or they can go out 'On Assignment' to foreign cities and do various missions or be given 'Counter-Intelligence' duties in one of your own cities.
I like how it looks like you can do more with your agents internally as well as externally.
National Security Projects
I wonder what other National Security Projects there are?
Insider Trading: X% boost to energy per turn for each agent at HQ.
Biometric Authentication: Increases chance that foreign agents are apprehended while undertaking Covert Ops in any of your cities.
Data Analysis: X% boost to science for each agent at HQ.
Cryptography: Speeds up information gathering for Agents undertaking Surveillance Operations out in the field and Surveillance provides high quality information more regularly.
Disinformation: Slows information gathering by foreign agents in our cities.
Black Ops: Energy is deducted from the economy proportional to number of agents in the field. Success chances for all Covert Ops are increased.
Strategic Analysis: Gives 1% boost to attack strength of your units when attacking units of chosen faction for each agent at HQ.
Internal Covert Ops
I also wonder if Agents in your own cities can be given specific missions as well as simply perform counter-espionage?
Humanitarian Aid/Hearts and minds - this mission can be performed in occupied cities to shorten resistance time and/or reduce unhealthiness for several turns.
Blackmail/Intimidation - this mission can be aimed at particular sectors of the population to temporarily boost performance. e.g. Blackmail Researchers - gives a boost to the science output of the city. Intimidate Labour Leaders - boosts production.
External Covert Ops
Agent travel and set-up times should be reduced by Open Borders and if you have an active trade route to the target city.
Infiltrate Station: Can our agents infiltrate Stations and disrupt their trade links with other colonies? Could an agent as a high-level operation instigate a coup in a station to turn it into an Outpost as an alternative to destroying it militarily? Losing whatever trading bonuses they were giving but gaining a city?
Blackmail Diplomat - worsen diplomatic relations between the city's owner and a target faction.
Assassination - kill high-profile target in the city to cause chaos and reduce the city's output in a particular sector for several turns. eg: Assassinate a celebrity to reduce culture, or a Trader to lower energy output, etc.
Smuggling Operation - gain access to 1 unit of a workable strategic resource within this city's radius.
Ambush Traders - sever trade route originating from this city.
Art Heist - Agent steals Earth Relic or priceless artwork giving a one-off culture boost to your colony and opponent colony loses that culture.
Sticky Bomb - attaches an explosive to an orbital unit based in this city that will detonate on launch or that can be remotely detonated later?
Bug Hunt - raises alien aggression level, blame for this is targeted at infiltrated faction.

So far we've snatched glimpses of early, low-level Covert Ops and the Affinity-locked missions:
Establish Network
Siphon Energy
Steal Science
Steal Technology
Dirty Bomb (Purity)
Worm Strike (Harmony)
Sabotage Mission (Supremacy)
The image above also shows a 'At Headquarters' section with:
"National Security Project: Propaganda - +1%(?) Health for each agent at Headquarters" with a button marked 'Switch Project'.
This suggests that your agents can be assigned to the National Security Project to affect your entire colony in various ways. Or they can go out 'On Assignment' to foreign cities and do various missions or be given 'Counter-Intelligence' duties in one of your own cities.
I like how it looks like you can do more with your agents internally as well as externally.
National Security Projects
I wonder what other National Security Projects there are?
Insider Trading: X% boost to energy per turn for each agent at HQ.
Biometric Authentication: Increases chance that foreign agents are apprehended while undertaking Covert Ops in any of your cities.
Data Analysis: X% boost to science for each agent at HQ.
Cryptography: Speeds up information gathering for Agents undertaking Surveillance Operations out in the field and Surveillance provides high quality information more regularly.
Disinformation: Slows information gathering by foreign agents in our cities.
Black Ops: Energy is deducted from the economy proportional to number of agents in the field. Success chances for all Covert Ops are increased.
Strategic Analysis: Gives 1% boost to attack strength of your units when attacking units of chosen faction for each agent at HQ.
Internal Covert Ops
I also wonder if Agents in your own cities can be given specific missions as well as simply perform counter-espionage?
Humanitarian Aid/Hearts and minds - this mission can be performed in occupied cities to shorten resistance time and/or reduce unhealthiness for several turns.
Blackmail/Intimidation - this mission can be aimed at particular sectors of the population to temporarily boost performance. e.g. Blackmail Researchers - gives a boost to the science output of the city. Intimidate Labour Leaders - boosts production.
External Covert Ops
Agent travel and set-up times should be reduced by Open Borders and if you have an active trade route to the target city.
Infiltrate Station: Can our agents infiltrate Stations and disrupt their trade links with other colonies? Could an agent as a high-level operation instigate a coup in a station to turn it into an Outpost as an alternative to destroying it militarily? Losing whatever trading bonuses they were giving but gaining a city?
Blackmail Diplomat - worsen diplomatic relations between the city's owner and a target faction.
Assassination - kill high-profile target in the city to cause chaos and reduce the city's output in a particular sector for several turns. eg: Assassinate a celebrity to reduce culture, or a Trader to lower energy output, etc.
Smuggling Operation - gain access to 1 unit of a workable strategic resource within this city's radius.
Ambush Traders - sever trade route originating from this city.
Art Heist - Agent steals Earth Relic or priceless artwork giving a one-off culture boost to your colony and opponent colony loses that culture.
Sticky Bomb - attaches an explosive to an orbital unit based in this city that will detonate on launch or that can be remotely detonated later?
Bug Hunt - raises alien aggression level, blame for this is targeted at infiltrated faction.