*SPOILERS*
Despite what Sam Tarly told Bran Stark/the Three-Eyed Raven in Game of Thrones's Season 7 finale, let's not forget it was Gilly who made that bombshell discovery about Rhaegar Targaryen's marriages. While reading through old records at the Citadel with Sam, she came across a high septon's personal diary entry that revealed Rhaegar annulled his marriage to Elia Martell and secretly wed Lyanna Stark on the same day.
Thanks, Gilly.
Though Sam overlooked the discovery at the time, he later brought it up when Bran revealed to him Jon Snow's real parents, Rhaegar Targaryen and Lyanna Stark. Since the two were married, per Gilly's findings, that means Jon is actually heir to the Iron Throne.
To prove her discovery, HBO released images of the High Septon Maynard's diary, including the entry where he records the big Rhaegar reveal. The pages are yellowed and a bit torn and the ink is slightly faded, but the important info is still there.
The legible parts of the entry read:
One to unforeseen events and … from setting down my record for … an annulment for Prince Rhaegar … marriage to Elia Martell … marriage to Lyanna Stark in Dorne. He forbid me to tell anyone of the ceremony so I shall not.
And, because as Gilly noted, he records every minute detail there's also a postscript about Maynard's one bowel movement of the day.
The last line, where Maynard admits to hiding the truth, is perhaps the most telling. While everyone else believed Rhaegar kidnapped Lyanna, he and the couple kept quiet, allowing an entire war take place over a falsehood.
Bran even makes note of this when he has a vision of their wedding: "Robert's Rebellion was built on a lie. Rhaegar didn't kidnap my aunt, or rape her. He loved her."
