A tracking weapon's projectile has a listed speed; once fired, it moves that number of hexes toward its target... if the projectile reaches the target's hex, it deals the listed damage.
In your example, the missile reaches the target and detonates the same round it was fired. If the target has point defense weapons in a suitable arc, then a gunner may attempt a special gunnery check to shoot down the incoming missile as per that quality, but it is otherwise impossible to do so. Point defense reaction checks specifically target a DC set by the missile's speed, but normal gunnery checks target AC or TL. A missile has neither, and there is thus no number against which to make a check.
When does the gunner roll to see if the missile hits? When he fires the missile, or when the missile makes contact with the enemy hex?
If the attack is made with a tracking weapon such as a missile launcher and the result of the gunnery check equals or exceeds the target's TL, the tracking weapon's projectile moves its speed toward the target. If it intercepts the target before it reaches the end of its movement, it explodes and deals damage as normal. If not, attempt a new gunnery check at the start of the next gunnery phase ot determine whether the projectile continues to move toward the target.
The gunner attacks as normal, targeting TL instead of AC. If they succeed, the projectile moves its speed away from the ship, detonating and dealing damage as appropriate if the target is in range. If the target is not within the projectile's movement range, it moves its speed, and the gunner makes another check vs. TL at the start of the next gunnery phase, with neither bonuses such as computers nor penalties such as range increments applied. This second step repeats until the projectile reaches its target or the gunnery check fails.
If the target is within the projectile's movement range on the turn it is fired, the only difference between a tracking weapon and a direct weapon is that the tracking weapon allows a point defense check.