Mr. Sinister's Study of the Summers/Grey Line in Action
Mr. Sinister was indeed a mad geneticist obsessed with genetics and bringing up humanity to its next level no matter what the cost. In a way, he is Darwinian but perhaps lesser or greater than Apocalypse. Having been centuries old, he had observed the Summers' line to which he would later cause some serious damage to the later parts of the future. He was the one who threw in the chess pieces that could have destroyed humanity especially when he examined the Summers' brothers, grew an unusual interest in Scott Summers and Jean Grey... and in two different realities, produced Omega Level telepathic beings thanks to his studies.
So how did his studies go? He developed a fascination over his soon would be archenemy Scott Summers. When he discovered that Cyclops' optic blasts could harm him at a higher level, he took his as a sign of new discovery. He grew obsessed with the Summers lineage and decided to play matchmaker one way or another.
It was later discovered that Mr. Sinister had actually also been interested with the Grey lines. He theorized that the offspring of Cyclops and Jean Grey would create such a powerful mutant. During that time, he wanted to also put Jean Grey under his custody, hoping to make both Cyclops and Jean Grey mate, produce a child for him but he failed to do so. In his case, he took a blood sample of Jean Grey and cloned her... producing his "daughter" Madelyne Pryor. He started to think she was a waste of his time, as she grew into maturity, she showed no mutant powers developed until the Phoenix Force descended into it. So he through some kind of weird science, programmed Madelyne Pryor with false memories as to get her to marry Cyclops in Jean Grey's place. Most people assumed Jean Grey had already died.
Everything worked as Sinister planned. It didn't take long for Madelyne Pryor to become a Jean Grey substitute. She even married Cyclops which led to a dysfunctional marriage of convenience. Cyclops married her as a substitute to Jean Grey (though events in The End suggest that he learned to love her). They had their son who was named as Nathan Christopher Charles Summers. Mr. Sinister influenced her indirectly to name the child Nathan, after him. During this time, she wasn't aware of her true origins until Cyclops abandoned her for his first love, Jean Grey which led to the events in Inferno.
Later events proved Mr. Sinister's theories right. Even as a child, Nathan Summers manifested such power that Apocalypse was awakened. Later, Apocalypse kidnapped the child of Cyclops and Madelyne Pryor aware this was a scheme by Mr. Sinister, infected the child perhaps to test its true worth. The child Nathan Summers was brought to the Askani Future where for some reason, time travel becomes risky. This action alone causes Nathan to be stranded there and leading to this...
An extremely convoluted case of Cable's return. Yes, Cable due to him being stranded in the Askani Future soon came back, double the times older than his father. In fact, Cyclops had to deal with the fact that the son he sent into the future, has now returned much older than him, even old enough to be his father! Later on, Mr. Sinister revealed to his "grandson" Cable that he was the real child and that Stryfe was a clone. Stryfe while being an uninfected clone was able to use that potential greater than Cable. Cable also played an important part in completing the family unit that required Cyclops Jean Grey and Cable... however Cable is the son of Madelyne Pryor.
Later on,a resurrected Madelyne Pryor would meet her own son in an uneasy truce. Here Madelyne explained her life as Mr. Sinister's clone of Jean Grey. Cable would fulfill the task he was ordained to do... defeat Apocalypse but later, he would also revive Apocalypse from the dead during Decimation.