YuGiOh/Stargate SG:1 fusion
The Millenium Items are Goa'uld devices. They were working on personality imprints which could take over bodies as necessary; different method of immortality, still taking new bodies, just less chance of them dying. The Rod only took basic characteristics and imposed them on its holder. The Ring held the personality, but the original owner of the body can fight back and regain control (not permanently, but he can't be permanently subdued either). The Puzzle was damaged (not outward damage, the internal components which can't be seen were destroyed in some of the pieces) and therefore Yami has no personal memories - to the point where he believes at first that he is a split-personality of Yugi, instead of knowing what he is. He is woken when Yugi is threatened, but does not take permanent control. The Eye is the most effective device, not least because it is physically implanted into the victim.
Their alignments (for want of a better term) work out as follows: Ring, Rod, and Eye: Goa'uld. Puzzle: leaning towards Tok'ra (sometimes). Scale, Key, Necklace: Tok'ra.
I have no idea how the game Duel Monsters can be made to fit in with this, but obviously it should. Pegasus revives the game FOR SOME REASON and that is what sparks the rest of them off. (Pegasus might even do it for that reason; now figure out why the game would wake up the others.)
If you want to bring in SG-1, do it; if you can't be bothered, or can't see how to, that's fine too.
Darklight/Thoughtcrimes x-over (slash, Brendan/Anders)
Freya and Brendan are assigned to see what they can find out about Anders Raeborne. They reach him before Anders has gone too far with the experiments - he hasn't actually killed anyone yet - and Freya manages to get through to him far enough that he stops blindly trusting Chapel.
Chapel takes exception to their interference with his plans. He somehow manages to infect Brendan and Anders with enough altered darklight to turn them both into demonicos. Freya can still get through to them both, but only Anders has enough experience of dealing with darklight infection to listen to her. [Anders controls his darker side with an image of the sort of relationship he'd really like with Brendan (lying in bed all afternoon just playing), because he knows that if he lets loose then he'll lose even the tiny chance he currently has of Brendan ever deciding he wants that.] Anders prevents Brendan from hurting anyone, and they both change back to human.
Lilith and Shaw find the three of them stood together, and Anders has a moment of total confusion over part of his mind saying, "Mom!" Brendan and Freya have grown quite protective of Anders by this point - Freya can see what his father put him through, after all, and Brendan is more than willing to trust her judgement. Besides, Anders is the one who got Brendan calm enough to change back. So they stand up for him against the newcomers.
Beyond that, it's up to whoever takes this on.