At the end of Halo 3, when The Ark exploded, the resultant energy changed the wormhole Master Chief was about to go through. As a result, instead of being left behind with half a ship, the whole ship (or maybe just half a ship instead?) gets transported somewhere else. That somewhere is the Citadel when the Reaper, Sovereign, warped itself there to wreck havoc at the end of Mass Effect 1.

With a whole ship at his disposal, John 117 joins the battle. Not much choice there. It's either that or get blown out of the sky.

With half a ship at his disposal, John 117 ends up crashing into the citadel itself, and he ends up joining the fight on foot.

Considering this is Master Chief we're talking about, either way, he's going to end up meeting up with John Shephard, and together they tag team Sovereign and its puppet, Saren Arterius.

Master Chief is pro human no matter where he is, so he'd most likely become an ally of the federation and probably get a spot on the Normandy.

Master Chief would want help returning home, so he'd end up getting involved with delving into the technology of the Protheans, or to be more specific, Cortana would while John keeps chauffeuring her around.

The very existence of Cortana and her role with the Master Chief is going to cause some serious concerns for everyone considering how they consider AI what with their compunction of going rogue like the Geth in their universe. That'll cause a whole slew of conflict that's going to need resolving.

Thanks to Master Chief's presence, The Normandy is going to be making some stop changes, so it may or may not get blown up by the Collectors.

If it does get blown up, Shephard will probably be saved by Master Chief.

If it doesn't… well either way, Shephard's probably going to survive, resulting in him being able to take steps with Master Chief to figure out how to stop the Collector's a whole year sooner.

Cerberus will probably step in with the Normandy Mk 2 at some point to try and get an 'in' with Shephard and his team so that the Illusive Man can get his hands on the Collector's Base as usual.

It could go either way whether Shephard and his team accepts help from the Illusive Man. Considering how much pussy footing the Alliance does, he probably will, and this time since Ash will be there, she won't be such a bitch about it… or maybe she will freak out about it and tell Shephard she can't follow him down this road or something… I'm not one for angst in my stories, but this is a Halo/Mass Effect cross over. Angst is probably going to happen just like in real life unless Tass shows up, but this isn't a Tassadar's Legacy story at the moment. If it was… well… *shrug*

If Tass shows up, you can bet that no angst or drama will be allowed if at all possible. Well… unless it happens to him. He's good at stopping the drama and angsting in others, but himself? He's a little less successful in that regard.

If Tass doesn't show up, Well… Master Chief and Shephard will just end up continuing the adventure, getting information on prothean and reaper tech in a bid to find a way back home. Perhaps having Cortana study the Mass Relays, especially the one on the Citadel, will prove useful, and may yield results. I imagine even if it did though, Master Chief would probably commit to the fight with Shephard until it's over. Though common sense would be for him to travel back and get reinforcements… though there's always the chance that a trip like that is one way…

Either way, in the end, Master Chief and Shephard fight the Reapers on Earth. Shephard gets smacked awake by Master Chief after the laser hits and they make it aboard the citadel, alone. They make their way to the central hub and activate the super weapon thingy.

God child shows up and tries to screw with their head with circular logic. Both shoot him down, along with Cortana getting almost vindictive pleasure doing so, considering the three choices that the stupid child tried to give. Master Chief decides to take option four by using Cortana to kick God boy's virtual ass, leaving the way clear for Cortana to do her thing, shutting down the Reapers with a large pulse of energy, that is in no way destructive so doesn't have any right blowing up anything. At the most it causes Reapers to collapse, crash, etc like a very selective EMP.

Thanks to this the battle is over, everyone cheers and celebrates. A huge intergalactic relief effort for Earth and all the other planets screwed over by the Reapers goes into effect spear headed by Shephard and his team. At this point, if John already discovered a way to go back home, he does so since his promise is fulfilled. He does agree to open talks between their two governments when he gets back home if he can find a way to return again. Considering Cortana now has a crap ton of knowledge of Mass Relays and such and how to build them, that's highly likely.

The End

-Edit-

Or not.

In the attempt to return Master Chief to his home, Shepherd and Master Chief end up transporting themselves into the Star Wars universe at the time of the Clone Wars. They hook up with Anikan Skywalker. Through their outside influence, they're successful in keeping him free of Sidious' influence, in particular Shepherd is helpful in this thanks to her experience with indoctrination.

While there, all three have various adventures with many supporting characters along for the ride as well. The Normandy gets some extra rehauling, getting officially reclassed as the Normandy SR-4, what with having both Edi and Cortana as cooperating AI on board the ship, though Cortana prefers to stick to Chief's armor.

The trio may or may not rediscover the Star Forge, and who knows what else other adventures they may uncover while trying to find away home, as well as helping their new allies out with their own war. Jedi Order may or may not get fixed without blood shed, seeing as the rebalancing of the force required the destruction of both the Jedi and the Sith.

At some point, the Citidel Council, or more particularly the human government anyway, may try to find a way to get in contact with Shepherd again, though this might be a little too AU considering just how much the lot of them dragged their feet on anything in the games.

In the end though, once everything is seemingly settled, and after getting more information and tinkering, the two may continue on, and Anikan will be stuck along for the ride, either by being sucked into the portal alongside in his own jedi star fighter, or possibly being on board at the time for whatever reason.

This lucky trio then gets to deal with the Starcraft Universe from the very beginning. They'll meet Jim Raynor at some point, they may or may not join the Sons of Korhol, Sarah Kerrigan would probably be rescued by the lot of them with the Normandy rather than let her be infested, but that may or may not happen. Either way at this point, these three, now four, are pretty much being thrown together and unleashed on this universe, so really the things they could do together at this point are many and varied.

After this point, the Protoss technology and information combined with everything they already have will probably enable them to give the SR-4 a proper Dimensional Drive, thus changing the ship to the SR-5, and allowing the connection of the four universes, for good or ill. Or not. Perhaps they decide that it'd be safer to drop them all off in their home universes then destroy the drive and go their separate ways, but these guys are too pragmatic for that in my opinion. They know that the knowledge for such a thing is already out there. At the least the Protoss would've figured it out through helping the build the D-Drive in the first place, so it'd be better to just take responsibility.

The story can really go anywhere the heck else ya want from there.