Alternation is the observation that two corrections inside one impulse are usually built differently. If wave 2 was simple and deep, wave 4 tends to be complex and shallow. And the other way round.
One thing first: this is a guideline, not a rule. Rules cannot be broken — markup that breaks one is inadmissible. Alternation is broken regularly, and that does not invalidate anything.
What exactly alternates
Three features are usually named.
Form. A simple correction (zigzag) against a complex one (flat, triangle, combination).
Depth. A deep retracement against a shallow one.
Time. A quick correction against a drawn-out one.
They need not all coincide: alternation is most often visible in one or two of the three.
What it is good for
As a tiebreaker between several admissible counts. If two versions pass the rules and one of them makes both corrections identical — both simple, equally deep, equally long — the other is usually closer to how real impulses look.
That is an argument for a version, not a proof. Impulses with two similar corrections exist.
What alternation does not give you
It does not say what wave 4 will be. Knowing that wave 2 was simple does not turn into a prediction of wave 4's form, depth or duration — it only makes some options more expected than others.
And it does not discard markup. An impulse where both corrections are simple and alike remains admissible: all three hard rules can hold in it.
A common mistake
Using alternation as a prohibition: "wave 4 cannot be a zigzag because wave 2 was a zigzag." It can. Alternation is about what happens more often, not about what is permitted.
The opposite mistake is ignoring alternation entirely and failing to notice that a count has come out suspiciously symmetrical. Two identical corrections in a row are a reason to re-check the scale, even though on their own they break nothing.