I'm of the opinion that regardless of what the rolls were when it happened, Silently should have just killed Danny off after the Behemoth fight.
My opinion is that dice rolls must be sacrosanct, since they offer a source of consequences that we cannot finagle our way around, so we have to take it on the chin and come back from it in another way. It's a great way of driving the story forward in a quest, where so much is under us the player's control. Since Danny is alive, that means he can still play a role in the story, and his current condition is not something that Taylor can fix by beating up bad guys or throwing more magic at it, so it's a different source of tension and conflict than the usual villain fights. At the moment, I can envision four possible narrative routes that could occur with his character.
- Danny could die. This closes his storyline and removes him from consideration. The aftereffects would be that Taylor would officially be an orphan, and would likely compound her guilt because Danny was injured at an Endbringer fight that she wasn't there for. While Taylor and co. are immune to Masters, good old emotional wounds are a tried and true way of manipulating people, so it's a potential weakness for the future.
- Danny could be healed in some manner. This would have us figuring out where Danny would fit in, since his power would be worthless on our team of mages and the Privateers are finished. He could join the Protectorate, sure, but an option we now possess would be to give him a Linker Core vial and then burn out his powers with a Device. This would also give us an instant candidate for the final template, no social maneuvering required, but does run the risk of making a mutant Danny.
- Someone uses Danny in his current state against Taylor. We've had info leaks bite us in the ass before, and the PRT and PHO know about a connection between Calamity Witch and Captain. Hell, if any of the Privateers survived the last foray against the Disney princesses (besides Kurt) and wants vengeance against Taylor for not helping, that would be someone perfectly poised to know who Calamity Witch is. If Danny was reported missing or kidnapped from the care centre, Taylor would rush to help him, and be possibly lead into a trap.
- Aceraptor's suggestion of Danny second-triggering, presumably into an S-class threat situation. Depending on how the power manifests, this could lead to a large portion of the city/the population being irreparably altered by the power, and could potentially cripple the heroes and PRT for the foreseeable future. Having Arcana and Taylor deal with Danny in this situation would further any "dark" reputation they have gained from dealing with the Fallen. Also, having to be the one to kill Danny will traumatize Taylor in a huge manner, and will likely have ripple effects both with her public persona and in private.
The Third and Fourth options could also have the consequences of Taylor getting unmasked/her information being made public. This would drastically affect Taylor, Lacey and Kurt, and Kayleigh and Laura since all of them could now be targeted or surveilled for more information, and it would negatively affect any future social situations, since associating with Taylor now runs the risk of being used as a hostage/spy by a villain group.
I definitely think the 'Unattended plotlines always have bad outcomes' thing is definitely one of the major issues. Neutral outcomes -at least for some of them- would be nice...
From a Watsonian standpoint, neutral endings are rare because Taylor is a superhero, so the issues she involves herself with tend to be villainous in nature, and villains being ignored generally tends to lead to negative consequences. Add to that the Shard's programmed conflict directive means that Parahumans by and large are never satisfied with the status quo and will continue to escalate until confronted. The Protectorate and PRT are hamstrung by bureaucracy, attitudes, and lack of manpower (am I remembering that Chevalier, Miss Militia, and Sere are the only heroes mentioned for Philidelphia + the three Wards?) and while Operation Pentagram does negate that somewhat, they are still being cautious so as not to trigger all the gangs/villains in the city to declare war against them. Also, if we don't get involved with a situation, we wouldn't notice or care if it has a neutral outcome, and while a positive outcome might garner some interest, a negative outcome is much more likely to force us to confront and deal with the issue.
The issue with neutral outcomes/positive outcomes from unattended plot lines is that from a Doylististic perspective, Taylor is the protagonist. The very structure of the story is designed so that Taylor has great relevance to the world, and therefore her absence has consequences. So while there are other crimes/events occurring in the city/world, Silently is presenting us with the ones that would significantly benefit from Calamity Witch's presence, and so therefore, by ignoring them things turn negative for those events. In addition, neutral and positive outcomes when we aren't there, well, they have a lessened future impact on the story. Ignoring the Fallen gathering at Brockton Bay gave us an entire chapter involving almost all the villains of Brockton Bay and multiple possible outcomes depending on our choices and creativity, which is excellent for a quest environment.