Here's where I think the entirity of Littlefinger's remaining plot arc is going to go: Sansa will soon marry Harry the Heir in private through Littlefinger. While that happens, the Bolton regime in the North collapses due to a combination of Stannis, the Manderlys, and the Watch/Wildings taking out Ramsay's men when he comes to collect his bride. Cersei will demand that the Vale and Riverlords go take back the North from the Northerners and Stannis. Littlefinger humbly agrees.
Littlefinger takes Sansa and the Vale's army with him, leaving Harry the Heir and Robert (if he's still alive) behind to watch after the Vale. Littlefinger picks up some of the Riverlands' lords and armies on the way (now being the Lord of the Riverlands) as well as intercepting some of the Frey hostages on the way to King's Landing. Eventually he arrives in the Twins to pick up additional Frey forces. Once settled, Littlefinger razes the Twins and kills all the Freys. Some of the Freys escape to the South, but are instantly killed by Nymeria's murderous pack. The Brotherhood Without Banners meanwhile wipe out the Freys at Riverrun.
Littlefinger claims Sansa as the Queen in the North and releases the remaining Frey hostages who all swear their allegiance to her. Sansa is incredibly disturbed by the actions taken due to the fact that no one but the hostages were spared, including the women and children. Littlefinger tells Sansa that she doesn't have what it takes in the end since she has the soft heart of a woman. Sansa then figures out that Littlefinger told Joffrey to execute Ned and is responsible for the destruction of her family. Also at this point, the remaining Lannister allies begin plotting to betray them to Aegon, and the Lannisters are basically destroyed after that (with the exception of possibly Jaime and definitely Tyrion).
Sansa and Littlefinger now make their way up to Winterfell with their whole army, but find the castle almost entirely abandoned. Stannis' previous garrison is now in the North fighting the Others, who by this point have broken through the Wall. Littlefinger finds out and Sansa overhears that Rickon and Bran are still alive, and that Jon Snow has been reborn and is leading all the troops in the North. He becomes much more physically abusive of Sansa at this point since this is the first time his plan has gone awry, even to the point of raping her. Sansa also figures that he is now plotting on killing her remaining family to secure Sansa's claim.
The day of reckoning finally comes, and the Others make their way to Winterfell. There is a brutal battle where all seems lost, but Tyrion riding Viserion and backed up by a portion of Dany's army come over the hill and turn the tide of battle. Tyrion demands their surrender and to unite their army with his, since it's the only way they can survive, or else he'll burn Winterfell to the ground. Sansa pleads with Littlefinger, but Littlefinger refuses and the battle continues, this time with Littlefinger's forces vs Tyrion's. Tyrion however doesn't go through with his word in burning down Winterfell since he respects the place too much and knows that the only person he needs to take down is Littlefinger himself.
Tyrion flies into the castle and sees Littlefinger running into the crypts. Tyrion runs after him. Down in the crypts, Littlefinger ambushes Tyrion nearly killing him. Littlefinger though begins to gloat and tell Tyrion how he outsmarted all his highborn cohorts the entire time, and how he tried to have Tyrion killed numerous times, knowing that he was his only real threat who could see Littlefinger for who he really was. Every time Tyrion would slip barely slip between his fingers, but each time it worked to his advantage. Tyrion surviving Catelyn ensured Harrenhal, surviving Ser Mandon (who he bribed to kill Tyrion) allowed him to take the blame for murdering Joffrey, escaping execution allowed him to kill Tywin and plummet the kingdom into chaos, and now he delivered a dragon to him personally to burn down the kingdom for good.
As he goes in for the kill, Sansa stabs him from behind through the heart with the Valyrian Steel dagger he framed Tyrion with. Littlefinger realizes his error too late and notices that he's at the foot of Ned Stark's tomb. Sansa then helps Tyrion to his feet and sees to his wounds with their Maester. They annul their marriage, unite their armies, and go to join Dany and Jon for the great final battle with the Others.
This post was edited on 6/27 at 3:23 pm