How about an emergency which results in the unintended release of a live weapon (they were on their way to a night range detail) and this explodes nearby fatally injuring MacDonald. An alternative might be that he is hit by falling wreckage after the daughter and her WSO are forced to bail out - uncontained engine fire at low level. Pilot and estranged Dad are both flown by Lossie SAR to I/Ness hospital, where connection between the two is made by medic and couple are reunited before clogs are popped by Dad - cue lots of weeping etc, roll final credits!
Whatever, you decide needs to be plausible but some may recall the TV play: 'Friday on My Mind' which was screened circa 1991. RAF brass got upset because 'implausible' plot suggested 'Visiting Officer' was - how can I put this delicately - being over zealous in his attention to the widow of an accident victim. However, this actually happened.
Old Duffer