Tomb Raiding
Ultimately the only way to destroy the Necron threat is to seek out their tombs and destroy them. This will, of course, be resolutely resisted by the Necrons and will result in fierce battles raging across the surface of a dead world with the option of playing low points games depicting assault forces fighting their way into the tombs. The C'tan are unlikely to tolerate such an affront from a lesser species and the consequences of such raids could become quite apocalyptic.
Necrons and the Eldar
Old Grudges
The Eldar are one of the few races that have real knowledge of the Necrons and the C'tan. They will not therefore make the mistake of underestimating the threat they represent. Moreover, whilst the C'tan will maintain a certain level of contempt for the Eldar, they do present a rare opportunity to strike at one of the creations of the Old Ones. Engagements between Eldar and Necrons are quite likely to occur in space, so campaigns can include a Battlefleet Gothic element. Cityfight can be used to cover battles on craftworlds, and Warhammer 40,000 for Necron attacks on Exodite worlds.
The Legacy of the Old Ones
The C'tan still have an abiding hatred of their ancient enemies, the old Ones. Although their civilisation is no more, it is possible that some degenerate descendants of theirs still live on backwater worlds. These rather tragic creatures are a choice delicacy to the C'tan so they attach a disproportionate importance to seeking them out. This can be exploited by the Eldar to ambush and destroy Necrons or to lure them from their tombs. You could even have some fun by using a Warhammer Lizardman army in a game of Warhammer 40,000, although this would require a bit of preparation to deal with any oddities.
Conclusion
Any game of Warhammer 40,000 will be more enjoyable if the characters have established personalities and the objectives really mean something. This is doubly so when dealing with villains such as Necrons, whose cold, implacable onslaught can only really be thwarted by the hot-blooded heroism of the living.