Some contact and critical missions already have sub-missions in them where you can acquire an item by pick locking safes etc or gaining xp from hacking a computer. With contact missions they're sometimes more indepth than that where you can get a key/card from somewhere to get another key/card to unlock or access a safe/computer to gain xp or an item, which I think is better as it's more challenging and you don't have to have pick locks or hacker.
This idea could be expanded further where a key/card you receive in one phase unlocks or grants access to an object in the next phase or one of the ambushers between mission areas drops a key/card that can be used in the mission area you're heading to, this means the players who take the time to kill them will be rewarded.
The rewards you receive from sub-missions are just common items so that exploiters won't stock up on a special item by aborting and redoing the mission. This problem could be solved by rewarding them at the end of the mission for example:
- The NPC you have to kill to complete your objectives has the key/card as loot so you can't leave without completing the mission.
- The item you have to find to complete your objectives is in the same place as the key/card so you have to take both at the same time (one good use for the 'Take All' way of getting loot).
- You find the code for the item instead of the item itself and once you complete the mission your operator replaces it with the item.
