Since missiles in boost phase consist primarily of highly flammable, high energy fuels, the slightest breach of their physical integrity means catastrophic destruction. (When big missiles explode on launch, their fuel unleashes as much power as a small nuclear weapon.) The televised holocaust of the space shuttle Challenger in 1986 was a dramatic example. Also, early malfunctions of attitude control systems send a non trivial percentage of missiles and space launchers out of control, forcing range safety officers to destroy them. Malfunctions of guidance systems are also not uncommon. The first flight of the Soviet Energia booster in 1987 ended up guided into the Indian Ocean (and the person responsible ended up in Siberia).
The earlier in boost phase that a missile is struck or malfunctions, the less energy is imparted to it and the greater is the deviation from the intended course. If, for example, the missile breaks or is broken before it tips in the direction of the target, its remains must fall directly onto the point of launch. The sooner thereafter the break occurs, the closer to the point of launch the remains will fall. But the common assumption that missiles intercepted during boost phase will fall back onto the country that launched them is valid only for early boost phase. The laws of physics (of inertia) require that a break that occurs near the end of boost phase will necessarily result in the remains—including the warheads, which may be intact—arriving just short of the target.
Destruction or malfunction of post boost vehicles affect above all the accuracy of the warheads. That effect can be drastic, however, since even a tiny deviation at intercontinental ranges can result in misses of hundreds of miles. Even more important, failure or destruction of post boost vehicles is likely to prevent the arming of the warheads. That is because the mechanisms that enable the warheads to explode are disabled when missiles are in storage and during boost phase, and are typically engaged only when the warheads reach the highest altitude of their intended trajectory. Hence destruction or impairment of post boost vehicles may result in warheads arriving more or less near the targets, but as inert masses.
The destruction of warheads after they have separated from post boost vehicles and before they reach the atmosphere means simply that the pieces into which they have been broken continue in their trajectory toward the target (as modified by the act of destruction). When the pieces reach the atmosphere however, they do so without the protection of an intact heat shield. That means that they are likely to be both burned and scattered. Radioactive materials from nuclear warheads would reach the ground, but the contamination would be confined to the nuclear materials themselves (none of the isotopes produced by the explosion) and hence would be minimal. Chemical or biological agents would be rendered harmless by combustion.
