It appears Hugh Jackman's Wolverine will face Mr. Sinister in his final outing.
Cinema Blend reports X-Men: Apocalypse director Bryan Singer let the detail about Sinister slip on the commentary track for the most recent X-Men picture. Specifically, the director mentioned the post-credit scene featuring a representative of the Essex Corporation obtaining a vial of Wolverine's blood from the ruined Alkali Lake facility is a direct connection the third Wolverine film.
Essex, of course, refers to Nathaniel Essex, the civilian identity of Mr. Sinister. A 19th Century scientist obsessed with genetics — often the genetics of the Summers family — he made a pact with Apocalypse to become immortal.
Wolverine 3 is said to be set in the future and could see Sinister tracking down the Wolverine for one last experiment, as Sinister's activities have taken him all over the mutant world. Cinema Blend also suggests he is the "mad scientist" character Richard E. Grant is playing in the film. Which, if true, is definitely a good bit of casting.
Wolverine 3 comes to theaters on March 3rd, 2017.