Which value do you use to parry?

If a warrior suffers a -1 to hit (fighting against Plague Bearers, a Dwarf Troll Slayer using the Ferocious Charge skill etc.) and rolls a natural 6, can this attack be parried? In other words, do you count the natural roll or the modified roll when making a parry?

You count the natural roll, no parry.

As a follow up, if rolling a 5, would the parry need 6, or would the adjusted value of 5 be enough to parry?

I could see room for interpretation of this situation. The rules state:

SPECIAL RULE
Parry: Swords offer an excellent balance of defence and offence. A
model armed with a sword may parry blows. When his opponent rolls to hit, the model armed with a sword may roll a D6. If the score is greater than the highest to hit score of his opponent, the model has parried the blow, and that attack is discarded. A model may not parry attacks made with double or more its own Strength – they are simply too powerful to be stopped.

So, is the to hit score different from the to hit roll? Granted we are splitting hairs here, and I tend to favour interpretations that simplify game play over having to remember all kinds of exceptions (so personally I would go with natural rolls), but if a Plague Bearer's Cloud of Flies is supposed to distract and weaken the attacks of opponents, would this not make an opponent's attack easier to parry?

Games workshop rules in general are notorious for their lack of attentiveness to consistency of language. The Mordhiem book and nearly all of the following published work about the game follows the pattern of using different terms to describe similar situations with no explanation as to what is meant. One can assume that 'to hit score' is the same as 'to hit roll' or argue that it is different. Both premises would be valid as far as I can tell.

The group I play with would treat the 5 as a roll of 5 so that you would need a 6 to parry, but other interpretations are equally valid as far as I can tell.

Under "parry" in the Close Combat section it says "[To parry] Roll a d6. If the score is higher than the number your opponent rolled to hit, the buckler or sword has parried the strike. Note that it is therefore impossible to parry a blow which scored a 6 on the roll to hit."

So there it is pretty clear you have to beat the number rolled. Mind you, when they wrote that section there were no plaguebearers in the game nor ferociously-charging dwarves. I think technically, no parry. But see what the people you play with think about a house rule.

-Michael