Ok so lets assume that the Necron with the MSS is charged. In the sub-phase the enemy player gets to decide the order of things that must be done at the start of the sub-phase. Will he challenge? If he doesn't then the Necron player can challenge in return, and then use MSS. If he does challenge then the Necron player can accept the challenge and use MSS.
What is the problem exactly?
On reading the relevant rules, both declaring Challenges and the MSS occur at the start of the Fight sub-phase. The player whose turn it is decides on the order of these two events.
If it's the turn of the non-Necron player, he can choose to have the MSS resolve first. Note that the use of the MSS is not optional. Even in the case of an optional piece of equipment or rule, however, the player who's turn it is can decide the order- he first says 'declare whether or not you are using your xx' then decides whether or not to Challenge.
This allows the non-Necron player to decide whether or not to Challenge, or who with, based on who the MSS affect and whether they resist them.
If the Necron player Assaults, he gets to choose the order. In this case he will probably want to declare a Challenge, then use the MSS. However, he might decide to do it the other way round- say to MSS a rank-and-file model, then Challenge to avoid being hit by the rest of the squad, and this is perfectly acceptable.
If there is any grey area here, it's whether a player can choose to have the MSS resolve between the player whose turn it is deciding not to Challenge, and the other player deciding whether or not to. I read it as both decisions being part of the same 'Issuing A Challenge' event, which would mean he could not- the MSS would resolve before both players declared Challenges, or after.