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I'm not a pilot but have always looked to the open skies with dreams and admiration. I think we need to unpack a few assumptions.
Weather (WX) has always been an integral part of aviation, as early as the lighter-than-air (ie hot-air balloon) days. The strength of human kind is no match to what nature can throw at us, and so instead we adapt to what nature gives us. On one hand, nature provides niceties like prevailing wind and thermals, to allow us to build runways pointing into the wind and for gliders to gain altitude. On the other hand, nature can decide that an Icelandic volcano shoots hundreds of thousands of tons of particulate matter into the air, grounding all commercial flights in European airspace.
Resilience becomes the objective, to safely operate revenue aircraft in the face of fickle natural phenomena. And this is achieved in a multi-layer approach, with resilience baked in at every step. The aircraft itself, the crew, the airports, ATC, and the regulators, they all are trained and briefed on known hazards, which is part of why commercial aviation is one of the safest modes of travel, sans maybe the elevator.
Unlike volcanic activity or windshears/microbursts, thunderstorms and lightning give plenty of warning through day-ahead WX forecasts, as well as onboard radar. These are not fool-proof -- for example, radar can be shadowed by nearby precipitation, hiding enormous thunder clouds beyond. But despite how terrifying it may sound to fly through a storm, it isn't impossible and certainly not unmanageable. But it does take preparation, and requires sufficient margins so that if anything starts to look awry, there's an escape path.
Often times, the escape path is just to climb away.
There are many things which are potentially catastrophic for aircraft: loss of engines, loss of pressurization, a lithium ion battery fire in the cargo compartment, a medical emergency while overflying the mid-Atlantic.
But while a gut-reaction would be to outright avoid risk, human endeavors can make no progress like that. So instead, worst-case planning means developing procedures for when not if something bad happens.
Aircraft are designed to take lightning strikes, and although the Boeing 787 uses a lot of composite material, it too has provisions for lightning.
Seeing as the incident here occurred on 17 March 2025, I wouldn't expect the Japan Transport Safety Board (JTSB; the air safety regulator, equivalent to USA NTSB) to have published a final report. There might be a preliminary report, but this is not that.
This appears to be a collection of ADS-B data, a mention of damage to a control surface, and a Twitter post about airline compensation due to diverting from Haneda (HND) to Narita (NRT).
Were it not for the control surface damage, this incident might have fallen below the threshold for reporting, since no source suggests there were injuries and I don't see -- having not watched the video -- an emergency being declared by the pilots. Diversions are not wholly uncommon, for a number of operational or WX reasons.
I think this is wrong, based solely on the robust safety culture in both the USA and in European airspace. Safety culture means that procesures are developed to manage risk, these procedures are regularly practiced, are updated with the latest available recommendations, and non-wilful deviations from procedure (aka mistakes) will be addressed by additional training, not by punishment.
As Mentour Pilot eloquently reminds viewers of his YouTube channel, if punishment were metted out for every mistake, then it's a disincentive to report mistakes, which makes safety worse for everyone, because nothing gets fixed.
No doubt, there are pilots which have operated grossly outside the bounds of acceptability, like flying an empty jet into coffin corner, or allowing a child to fly the plane. Such accidents are reported precisely because they blew through every layer of the Swiss cheese model of accident causation, and tragically took lives.
So with all that out of the way, I think we can still try to answer the titular question.
A scheduled passenger airliner tries to get passengers from airport A to airport B. A lot of prep is done in the background to make this happen, organizing the ground crew, flight crew, and backend operations at the airliner HQ. Most of the time, the flight is uneventful and arrives as expected. A few times, there might a go-around, but pilots are trained to not shy away from doing a go-around, and have the reserve fuel to do so.
With any sort of damage on approach, be it from a bird strike or lightning strike, the pilots will have to: 1) secure the plane, usually by initiating a go-around to buy valuable time and get away from the ground, and 2) assess the condition of the airplane and make a plan. In this case, the airplane diverted to a nearby airport, which was probably the backup destination airport.
As mentioned before, WX is fickle, and a storm can easily creep over the airport when the plane is within radio contact. And even if the storm was already over the arrival path, if the indications are still suitable for landing -- eg low crosswind, no tailwind, no predicted windshears, no prior pilot reports of landing troubles -- then the pilots will have discretion to continue their approach.
For a healthy safety culture, the airliner's own procedures have to place the pilots as the ultimate decision-makers once a flight is underway, and so while it's unfortunate that damage occurred unexpectedly, nothing from the minimal available information suggests this amounts to a systemic or procedural error, nor wilful malfeasance.
The fact that the airliner returned to service days later means this might simply be slightly more than mundane happenings. Though it would be prudent to keep an eye out for a future report from the safety regulator which would may have recommendations for updating training or to the manufacturer to address a systemic fault. But sometimes final reports have nothing to recommend (rare, but it happens).