I try to avoid running GM-PC's (significant NPC's that accompany the PC's and participate in their adventures) if I can avoid it, preferring to keep the focus on the players and their characters. However, sometimes "needs must", and I'll run one or more of them while it makes sense to the emerging narrative. The following significant NPC's accompanied the party at various points in their adventures.
In an arc of the campaign, two different groups of the variants in alternate timelines are trying to find the Lost Caverns of Tsojcanth in the World of Greyhawk. Primarily, they seek the Crook of Rao.
A trio of significant NPC's initially accompany the group, representing the interests of the churches of Rao, Heironeous, and Cuthbert, Riggby the Patriarch of the church of Boccob the Uncaring, and the nations of Veluna and Furyondy.
The most powerful and stalwart of the trio is Sir Gralston, who has the quirk of being so consistent that all variants of him are exactly the same in every timeline.
Next most potent is an agent dedicated to Rao, who only engages in conflict when it can't be avoided or against true evil. Thus far two variants of this character have been encountered, the archly urbane Markis and the hyperfocused and nearly monosyllabic Sarkis.
The last of the trio is the friendly Lord Bannik Vorl, a youngest son of a border baron of northern Furyondy, and a favored agent of the king. The nominal leader of the expedition due to his royal writ and noble birth, he was killed in an early encounter, but in one timeline he was reincarnated as an Orc while in the other he perished.
Later, when the glitches successfully discovered the entrance to the Lost Caverns, a dimensional shearing event occured. After which, on the reality thread the story focus moved to Gralston had perished in the Underdark in a heroic blaze of glory to buy the party time to escape. Bannik, openly a Proctor for King Belvor rather than merely bearing a writ, is still alive and nominally in charge of the expedition. And the represenative of the Church of Rao is a samurai-like paladin named Marcus, a quiet man who counsels peace and rebukes violence.