John (II): last seen getting pulled into legendary planet with cortana
Kelly (II) : in Onyx's dyson sphere
Linda (II): same as kelly
Fred (II): same as kelly and linda
Lucy (III, beta company): Same as above
Tom (III, beta): same
Mark(III, Gamma): same
Olivia (III, gamma): same
Jun (III, Alpha, Noble): unknown
Rosenda: (III, unkown, Noble): unkown.
Gray team (II): Unkown
Black team (II): unkown
[/spoilers]
As for brutes: There were no brutes in the ships that were sent after the PoA at Halo, or they weren't sent out on the surface, due to Elites not trusting them.
The datapads? As best we can tell, they were made by a group of joined AIs that manuplated the UNSC for a few hundred years. See here for more details: http://www.forwarduntodawn.com/triumvirate-see-no-evil/
The Elites most likely became neutrally aligned with humanity, sharing a very limited amount of tech, and contued to try to hunt down brutes.
The jackels probably ran off as soon as they saw they were losing, some returning to their moon homeworld Eayn (Interesting note: while Eayn is fictional, the planet it orbits is not, it exists in real life, and is actually a potential planet for lie, fancy that?), some trading supplies with humanity (they are a capitalistic race, they already have done so in the past), most returning to their old ways as pirates.
Grunts most likely returned back to their home planet, while a very small amount would probably keep in touch with humans, they have expressed intrest in human culture before.
The drones and hunters would almost without a doubt just go back home.
The brutes would just splinter off into warring tribes, some would try to maintain control over whats left of the covenant.
engineers would stay whoever they were with at the time, if any prophets are still alive, they will be hunted down by elites.
The UNSC has no reason to hunt any down, they are barely functioning, and would rather make peace with them then anything.
The Halo's cannot be used to target a certain area or group of people, it'd be like trying to wife out a ameobea by nuking a zoo.