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Happy to clarify. (One of the challenges of the 24XX format is trying to cram a lot of gameplay into very little space!)

In the Saving the Day section, the numbers in the parenthesis are Linked Crises (from the same list) for that Crisis. If the Nightingales are trying to address an aspect of that Crisis with a roll and the result is a Disaster, one of the options the GM has is to start up a second Crisis.  The GM of course has the full freedom to spin up the Crisis of their choice, but the numbered Linked Crises in parentheses are the ones that seemed to make the most sense to me and are provided as guidance.

For example, Fire is the number 1 crisis on the list. When the Nightingales rush in to try and resolve a Fire crisis, the GM might give it the "walls of flame" and "trapped firefighters" aspects. A player in Nightingale-5 declares they're going to push through the walls of flame in the area to rescue the firefighters trapped in a warehouse and get them clear...but when they roll the skill die, the result is a 2--a Disaster! That triggers a second Linked Crisis that the Nightingales will have to address before the situation can be completely resolved.

The GM checks the listed linked crises for Fire: (12, 15, 17). Looking at the Crisis list she sees that 12 is 'Industrial Accident', 15 is 'Structural Failure', and 17 is 'Explosion'. Since she had already said the firefighters were trapped in a warehouse, she decides that the Structural Failure makes the most sense. She doesn't feel like things need to get too out of control (she wants to keep the story moving), so she only gives this second new Crisis a Crisis Level of 1--meaning it only needs one aspect.

She chooses "crumbling concrete" and tells the players that the heat of the flames has caused the concrete of the warehouse to start to break down. Not only do they still need to rescue the firefighters, they need to prevent the entire building from collapsing!

Hopefully that explains things more clearly.