Tears and Rain by SeulWolfe on FanFiction.net.
It is a story where the Malfoy family finds out that their son in law, Harry is being abused by Draco. Draco is later arrested and disowned.
Sadly, with each negative report, things began to go progressively downhill, and Harry began to show signs of weariness and avoided being touched. He became quiet and withdrawn, sometimes spending days in their suite, no matter how Cissa and Dobby tried to coax him out with promises of his favorite foods and pastimes. When Harry refused to see the Weasley-Grangers when they visited, Lucius had had enough, and forced his way into their suite and happened to catch Harry coming out of the bath. His blood ran cold at what he saw; the bruises that covered his son-in-law's body; everywhere except his face, hands, and belly. It certainly explained why the young man had been so withdrawn, and kept himself covered from throat to wrists, to the floor, eerily reminiscent of Severus' usual attire.
That day, he had locked his son in the study with him and all but threatened him with the 'Unforgivables' if he didn't cease the mistreatment of his bonded. That behavior was no longer acceptable in the Malfoy Home, and hadn't been since Lucius and his brothers, were children. Well, tonight, they had proof that it hadn't stopped. Draco had just become more sly about it, obviously manipulating Harry further to cover it all up. Now, he and Cissa prayed that Harry would survive. Draco had disappeared to Merlin knows where, and as angry as Lucius was at the moment, it would be a wise idea if he stayed gone for several days.
Tears and Rain, Chapter 1
Harry becomes pregnant.
"I never said you were ill, Harry." Neville rocked on his heels a bit and glanced at Narcissa as his serious expression became an amused one. "What you are experiencing is perfectly normal for a wizard with your physical make-up... you're expecting."
"WHAT?! I'M WHAT?!" Harry demanded, positive he'd heard Neville wrong.
"Pregnant, darling. You're going to have a baby. I'm going to be a Gran'mere. Isn't it wonderful?" Narcissa was beaming.
Tears and Rain, Chapter 32