After the first level, of the escape from Area 51 (Groom Lake), Agent Carter is brought to The Bureau's main base. From the Operations Room console, there are three kinds of missions accessable.
Major Operations are the main plot-driving missions, and require some activity around the base to progress. On the Mission Map, they are marked with a Sectoid head with two flags.
Minor Operations are supplemental missions, and the main source for equipment and experience for Agent Carter. Some Minor Operations need to be unlocked by performing certain tasks in the Base. They are marked by a Sectoid head with one flag.
Dispatch missions appear after each Major Operation, and some can be unlocked like Minor Operations. Agent Carter does not go out on these missions. Instead, any spare agents are sent out in their own squads, up to 5 Agents of any mix-- providing that their combined level matches or exceeds the "Mission Complexity" rating (ie: a rating of 8 can be performed by two Level 3 Agents & a Level 2, or two Level 4 or Level 5 Agents). After Agents are assigned to a dispatch mission, Carter himself must go out and complete a Major or Minor operation. When he returns, the Dispatch mission will also be completed. The rewards of such is that all sent Agents gain a level (if they have not maxed out at level 5 already), and a reward that is listed in the Mission's description. Rewards include a new mid-level agent, or a new Pack type. Dispatch Missions are marked with a silhouette of a charging soldier.
Lastly, there are Base Investigations: after every major operation, take the time to look around the base and talk to people, and watch the antics of the various agents, soldiers, and scientists hanging around. Some encounters will open these side quests. When you get one, pay attention to what the Objective notice says in the top-left corner, and the dialogue, to see what you need to do. Don't forget that the F5 button shows Objective locations: in the case of Investigations, the icon is blue, as opposed to a yellow icon for storyline progression in the base and forward progression while on a mission.
List of Missions on the Bureau: XCOM Declassified.
- The Doctor - Major - Rosemont, Georgia
- Grifter - Minor - Indianapolis, Indiana
- Guardian - Minor - Great Falls, montana
- Codebreakers - Minor - Bend, Oregon
- Not of This Earth - Major - Medford, Oregon
- Firestorm - Minor - Santa Cruz, California
- Hawkeye - Minor - Middle Valley, Tennessee
- The Last War - Major - Chicago, Illinois... (Spoilers)
- The Day the Sky Fell - Major - Mothership (Final Mission)
- Find the Missing Silacoids - Unlocks Deployment: Nanotechnology
- Talk to Dr Dresner in the back of the upper floor of the lab. He'll ask you to hunt down some escaped Silacoids. Use battlefocus to see their trails. Head out of the lab area, one will ambush you in the containment door. Continue to follow the path. Go to the bathroom. Follow the trail to the security gate upstairs. Kill the silacoids. Return to Dresner.
- Sleepwalkers - Unlocks Deployment: Sleepwalkers
- Find Dr Dresner near the lounge. Go to Ops, Engineering, Ready Room, Lab. go into battlefocus and use scan. There's an infected in the ready room, the other in the lab (near the Elerium silo). Dresner is now where he was in the previous investigation.
- Keeping Things Secure - Unlocks Deployment: The Russian
- Can be done when you scan Engineering for the other investigation. Simply go talk to the captive Russian, and choose "work with me" when prompted.
- Vendetta - Unlocks Deployment: Vendetta
- Continue with main storyline until Weaver steals a Skyranger and leaves for Oregon. Talk to Chulsky in comms (office across from yours), then to Percy in the Ready Room. Go to Angela's office, take down the Skyranger poster, inspect the safe, inspect the photo in the filecabinet in the corner, open the safe, and inspect the documents. There's no confirmation notice, but the deployment is now available.
- Flight Test - Unlocks Deployment: Flight Test
- Barnes is in Engineering, talk to him. Go into the hangar, battlefocus. Scan the leaks one at a time (you may need to reposition yourself to target properly). Barnes asks you to shut off the valves connected to the damaged pipes, like a 3D maze. The correct valves are: top-left one inside the Avenger, and the two on the left and the right in the row of panels to the right of the craft. Talk to Barnes again to finish.
- Cure - Unlocks Deployment: Cure
- Find Dresner in the front of the Lab area. Go to Dr Hara in the upper-back of the labs. The patient will be either Nico, or a random soldier if you allowed Nico to kamakaze himself. Talk to the patient. The correct choices are: "Time to wake up", "We're about to win the war", "Come on, it's me, Carter." Talk to Hara, then Dresner again.
- Gearing Up - Fernley, Nevada - Reward: Guardian Pack - Complexity: 5
- Nanotechnology - Bow, New Hampshire - Reward: Stabilization Assistance Pack - Complexity: 7
- Recovering Leaders - Fairfax, Virgina - Reward: Rank 3 Recon - Complexity: 7
- The Russian - Pima, New Mexico - Reward: Rank 4 Engineer - Complexity: 8
- Sleepwalkers - Des Moines, Iowa - Reward: Point Blank Pack- Complexity: 8
- Vendetta - Pendelton, New York - Blast protection - 9
- Flight Test - Fort Bragg, California - Quick Charge - 10
- Cure - St. Albans, West Virginia - Reward: Rupture Pack - Complexity: 10
- Behind Enemy Lines - Shreverport, Louisiana - Reward: Rank 3 Commando - Complexity: 10
- Claiming What's Ours - Seattle, Washington - Corrosive Plasma - 10
- Space Junk - Upland, California - Health Converter - 10