Checking is doing something to prevent and limit an opponent's options at a specific time.
Example:
If you are Kung Lao and your opponent is Liu Kang.... if Liu Kang does his 3hit low string, you block it, and you believe he might go for it again, you could CHECK him throwing out a spin or low jab.
This check will prevent him from doing any other option besides block or jump away.
Harder Example:
If you're Johnny Cage..... you do a move on your opponent that gives advantage on block(like his F32), they block it like you thought they would, then you throw out a low jab to CHECK your opponent in case they try to attack you back even though you have advantage.
Sure, after they block the low jab the opponent will be at the advantage though because having your opponent block a low jab leaves you at the disadvantage. But if you scare them into thinking you might do a low jab(Johnny's fastest move) they might look out for it and keep blocking. Since you know they are going to keep blocking you could throw out ANOTHER move that has frame advantage on block(like another F32).
Doing F32 then doing a F32 right after COULD be interrupted by the opponent's low jab because the startup on F32 isn't that fast, but this is why you should CHECK your opponent when possible in case they try to be clever and interrupt you while you have the advantage.
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PS: Don't think these terms were just made recently for Mortal Kombat. They're been around for years and years and apply to every single fighting game that's ever been made.