"Into the Breach" uses "capital A" Alignment.
Everyone -- and I mean everyone -- who has always lived upstairs and has never encountered a basement dweller or piece of basement tech is Unaligned. It doesn't matter how "good" or "evil" they are in colloquial terms.
However, Long Stair veterans often come back up... changed. Aligned somehow to weird forces. In fact, one way to test whether you're dealing with a basement dweller in disguise or long stair acclimated individual is the tried and true set of detect alignment spells.
You may choose one of the standard D&D alignments for your character, or you may choose to have remained Unaligned.
The conspiracy recruits both aligned and unaligned individuals -- they can hardly avoid it -- but aligned agents are watched more closely than those who went down and returned unaligned. Aligned individuals are connected to a still poorly understood xenocosmic war or fate of some kind, and that makes a lot of folks upstairs more than a little nervous. Observational reports also suggest that their actions, when driven by Alignment, may increase the likelihood of breaches. They have to be monitored, and any unaligned individuals on a team will be assigned to monitor the aligned ones for possible breach-provoking behaviors.
Agents and Psychological Health
Similarly, the conspiracy keeps a close eye on any signs of "Underground Acculturation Syndrome" (UAS), a syndrome of behaviors and psychological traits that appear to be a form of basement-specific PTSD, and that soldiers sometimes refer to as "going native" or (in more extreme cases) "going full murderhobo." Development of an alignment is one sign of the potential for developing UAS. Another indicator of UAS is the display of a marked preference for archaic weaponry and tools. Other, more serious behaviors, may develop. The conspiracy has very strict rules against agents looting the dead, as this behavior in particular is associated with UAS, and its occurrence is correlated with the creation of new breaches. The maintenance of real human relationships, in particular familial relationships, appears to act as a countermeasure, which is one of the reasons that agents are never employed full-time as counter-breach operators and are rotated through cycles of activation and rest. Rest phases are extremely important to the maintenance of psychological health. Team members are encouraged to report risk factors for UAS in their colleagues in an effort to get them counselling and appropriate help as soon as possible. In practice, team members sometimes cover up signs of UAS in their colleagues, failing to report indicators of the syndrome. There are known cases of entire teams going rogue, and in most of these cases, UAS has been implicated.
The conspiracy tacitly allows for some levels of (properly managed and balanced) UAS in its agents, however, in part because some level of UAS is unavoidable in agents and in part because it is often those agents who display signs of UAS who are the most effective operatives.