Well this is just a thought but think of this... im going to piece this together by chronology of advents...
1. Stryker's plan to make the ultimate weapon "Weapon X" wasnt just his idea, and he certinaly not the only character who was working on this...On the day wolverine was transformed into weapon x. The Facility staff includded Stryker, Cornelius, Carol Frost... and it was supposibly rumoured that Dr.Nathaniel Essex was there. There was a rumour that an actor said he had the role and he was actually in the movie. It was brief but there was a guy in the background black hair, wore a blue shirt with a black tie... when wolverine was in the tank... you cut to all the people that was there. He is the guy that finds wolveriens heart beat on the machine... later he interupts a converstaion between stryker and munson or stryker and cornelius... i cant rememer which. But that guy im sure was the same actor that said he was cast as Sinister...Either way i say, let that be true. and go with that. Dr.Nathaniel Essex is obsessed with making the ultimate weapon... when wolverine escaped weapon x facility was shut down. However Dr.Essex work would then continue seperately...
2. During x-men 1 - Dr.Essex helps Magneto create the device that change humans to mutants... again working in the background
3. during x2, Dr.Essex was the guy that was able to help re-instate Stryker to continue his quest to make the ultimate weapon however stryker had other plans and decided to try and wipe out all mutants. However Dr.Essex remained in the background learned of the location of Wolverine. the original ultimate weapon. By the end of the movie Dr.Essex learns of the ultimate power that cyclops has and the telepathy of Jean Grey.
4. During the third movie, Jean whilst in a coma state manifests the Phoenix persona - which is just an illusion by her subconcius mind...During the events of the war between humans and mutants on alkali lake, Dr.Essex finds Cyclops in a paralised state in the near by forest of alkali lake, his mind is completly wiped but this is because Jean is protecting him from the phoenix still in an unconcius level, When wolverine supposidly kills Phoenix... Jean awakes from the bottom of alkali lake and is found by Dr.Essex who was monitoring the area.
Firstly i just want to say although phoenix was a manifestation of jeans mind in my idea, jean grey is a telepath and teleknesis... so although she was projecting the image of the phoenix, when the phoenix de-atomized things it was actually coming from jeans body which is still at the bottom of alkali lake all done subconciusly but because her powers have become greater than xaviers... she is able to do what she did.
anyway back to the story...
So sinister has Cyclops and Jean, storm and wolverine try to continue unaware of there existance but think of this... we then bring in Gambit, who falls for Rogue, he is a bit older than her and remembers wolverine. Wolverine wanting to remember his past delves into Gambits past, and we learn of Dr.Essex and Gambits transactions which peacing the puzzle together leads to wolverine wanting to seak out Dr.Essex...
To top that... we have Dr.Essex create a new Ultimate weapon only this time Cyclops and Jean's powers are combined to make a mutant child.... now i was thinking either X-Man! or Cable! see X-Man would make sense because he is the product of Sinisters merging of both jean and Scott. But that was to take down Apocalypse... However we could have a young Cable born and have Wolverine fight Cable only to have cable turn against sinister... but it wouldn't make sense because sinister has not really had much involvement with Cable.