Microsoft's SCL Score is the level of confidence that Microsoft believes the message to be spam. This is stamped by O365. While Agari determines its own score based on message headers, URIs, and attachments, it does not take the SCL score into account while grading the message. However, if Microsoft has already labeled the message as spam with an SCL score of 5 and higher, Agari will by default skip scoring the message, resulting in the message not showing in the portal. By default when Microsoft scores a message as spam it is sent to the Junk Email folder. Microsoft has documentation where you can learn more about SCL, see Spam Confidence Level in EOP.
As Agari learns from email traffic, not analyzing messages already labeled and actioned by other security controls allows our data models to focus only on messages getting past other security controls. You can override this "skip" by navigating to Manage > Organization > Processing Exceptions and selecting the SCL score you would like to ingest.
If you would like to be able to view "skipped messages" without ingesting them, please contact support at email@example.com