Incognita can use programs to assist the agency in various ways. Programs are roughly categorised as PWR generators, firewall breakers, and utility programs.

You begin the game with a choice of one generator and one breaker. Additional programs can be acquired from Server Terminals and Research Databanks. One program, Turing, is acquired only in the OMNI Mainframe mission.

Incognita has slots for up to 5 programs, or up to 6 programs after the OMNI Foundry Lab mission in the extended campaign.

A generator is a program which generates PWR. If not stated otherwise, these programs generate PWR at the start of the player's turn. Generators are either passive, meaning they generate PWR automatically without the player's intervention, or active, meaning they only generate PWR when the program is used.

	Program	Value (CR)	Cooldown	PWR cost	Description
	Abacus	400	—	—	Generates +4 PWR at the start of every mission.
	Abacus 2.0	550	—	—	Generates +6 PWR at the start of every mission.
	Burst	300	2 turns	0	When used, it generates +3 PWR, and agents get +3 AP for one turn. While on cooldown, agents have -3 AP for two turns.
	Cycle	750	—	—	Resets PWR to 3 at the start of each turn.
	Dynamo	1000	—	—	Generates +2 PWR per turn, starting at alarm level 2.
	Emergency Reserve	300	3 turns	—	Generates +5 PWR at the start of the turn, if PWR is 3 or less.
	Faust	300	—	—	Generates +2 PWR per turn, but also a 20% chance of triggering a random daemon.
	Fusion	300	4 turns	5	When used, it costs 5 PWR, then generates +3 PWR per turn for the next 4 turns while on cooldown.
	Power Drip	300	—	—	Generates +1 PWR per turn.
	Root	300	6 turns	0	When used, it generates +6 PWR, then -1 PWR per turn for the next 6 turns while on cooldown.
	Seed	350	—	—	Reduces the PWR cost of the first program used per turn by 4.
	Siren	-	—	0	When used, it generates +3 PWR, but also raises the alarm tracker by 1 step. Cannot be used after alarm level 6.
	Wildfire	400	1 turn	0	When used, it generates +5 PWR, but increases firewalls on all devices by 1.

Found in the Contingency Plan DLC.
Found in the Nintendo Switch edition.

A breaker is a program which breaks the firewalls on mainframe devices. Most breakers are instant, meaning they break firewalls as soon as you use them.

	Program	Value (CR)	Cooldown	PWR cost	Description
	Brimstone	450	—	3	Breaks 1 firewall. Passively gives +10% chance of daemon reversal.
	Cricket	-	-	3	Breaks 1 firewall, and creates a noise which distracts guards in a radius of 4 tiles.
	Dagger	450	5 turns	1	Breaks 3 firewalls.
	Dagger 2.0	650	4 turns	3	Breaks 5 firewalls.
	Data Blast	400	—	3	Breaks 1 firewall on all devices in a radius of 5 tiles.
	Flare	450	3 turns	0	Breaks 4 firewalls, but increases firewalls on all devices by 1.
	Golem	500	—	≤ 4	Breaks 2 firewalls. The PWR cost is reduced by 1 each turn it is not used, and reset to 4 on use.
	Hammer	600	3 turns	5	Breaks 5 firewalls.
	Lockpick 1.0	300	—	2	Breaks 1 firewall.
	Lockpick 2.0	700	—	3	Breaks 2 firewalls.
	Mercenary	600	—	2X	Breaks 2 firewalls. The PWR cost is increased by 2 on each use, and reset to 0 at each alarm level.
	Oracle	500	—	4	Breaks all firewalls on a random Security Camera.
	Parasite	400	—	X	Infects a device to break 1 firewall per turn. The PWR cost equals the number of hosted parasites.
	Parasite 2.0	500	—	X + 2	Infects a device to break 2 firewalls per turn. The PWR cost equals the number of hosted parasites plus 2.
	Parity	-	-	-	-
	Rapier	600	—	X + 1	Breaks 1 firewall. The PWR cost equals the current alarm level plus 1.
	Ritual	-	—	1	Breaks 1 firewall, but triggers a random daemon. Passively gives +5% chance of daemon reversal.
	Turing	—	3 turns	5	Breaks 2 firewalls on all devices. Only available in the OMNI Mainframe mission.
	Wrench 2	600	—	2	Breaks firewalls if the device has exactly 2.
	Wrench 3	600	—	3	Breaks firewalls if the device has exactly 3.
	Wrench 4	600	—	4	Breaks firewalls if the device has exactly 4.
	Wrench 5	600	—	4	Breaks firewalls if the device has exactly 5.

Found in the Contingency Plan DLC.
Found in the Nintendo Switch edition.

Utility programs have various other effects.

	Program	Value (CR)	Cooldown	PWR cost	Description
	Aces	600	3 turns	2	Reduces the armor of all TAGged guards by 1 for one turn.
	Bless	500	—	—	Reduces the duration of daemons by 2 turns, to a minimum of 1.
	Charge	900	—	—	Reduces PWR cost of other programs by 2, but increases their cooldowns by 1 turn.
	Daemon Sniffer	350	3 turns	0	Reveals the daemon on a device, if it has one.
	Fool	100	1 turn	0	Reboots a device for 1 turn, but triggers a random daemon. Passively extends the durations of daemons by 1 turn.
	Hunter	550	3 turns	5	Removes the daemon from a device.
	Leash	500	—	—	Hacked drones stay controlled for +1 turn.
	Lightning	800	—	8	KOs a TAGged guard for 2 turns, but removes the TAG.
	Overdrive	700	—	—	Reduces cooldowns of other programs by 2 turns down to a minimum of 1 turn, but increases their PWR cost by 1.
	Ping	450	4 turns	1	Creates a noise which distracts guards in a radius of 4 tiles.
	Rogue	300	2 turns	2	Reveals an undiscovered Corporate Safe.
	Shade	500	2 turns	1	Reduces vision range of all guards by 2 tiles.
	Taurus	400	—	2	Moves a daemon to a random other device.
	Wings	500	2 turns	1	Gives all agents +2 AP for one turn.
	Wisp	300	—	3	TAGs all visible guards.

Found in the Contingency Plan DLC.