Mary refers to an incident in Sokovia. Sokovia is a fictional nation in the Marvel Universe. It features heavily in Avengers: Age of Ultron (2015), the events of which led to the Sokovia Accords, which called for the registration of all super-powered individuals.
This episode's title was taken from Marvel Premiere #17 (1974).
Colleen says "you've crossed the Rubicon, Danny". The Rubicon is the river Julius Caesar crosses in 49 BC which marked the beginning of the Roman Civil War.