Game of Thrones has been instrumental in the growth of what is known as "spoiler culture," partly due to the communal watching experience that's grown up around it. The series' shocking twists, experienced together on social media, is one of the things that make the show tick. Season 7 ended with a big surprise, revealing Jon Snow is not only the son of Rhaegar Targaryen (a long-suspected development) but this legitimate heir. Moreover, this Varys Game of Thrones theory suggests he could vouch for Jon's parentage in the final season.
Varys is one of those quiet survivors in King's Landing, a fixture in the shadows. This "Master of Whispers" was the Targaryen regime's spymaster for years before Robert's Rebellion, and somehow he miraculously retained the position after the Baratheon takeover. When the show begins, he's one of Small Council, a power broker who seems to be working in good faith with the current ruling family when Ned Stark meets him.
Over the seasons, fans learned otherwise. Varys is loyal to the Targaryen family, watching Daenerys' rise from afar. From Season 5 onwards, he openly works to pave the way for her return. However, Varys willingness to back whichever horse will save his skin has not gone unnoticed. In Season 7, Daenerys worries he could turn back to the Lannisters. What she should fear is him backing Jon Snow.
When Bran reveals Rhaegar and Lyanna married, Sam realizes he has proof Rhaegar's first marriage was annulled. Both believe this was done in total secret. But Crown Princes don't invalidate their marriages and set aside heirs unnoticed. At least, not by those watching the ebb and flow of power.
In the A Song of Ice and Fire novels, there's a line spoken by Tywin that, in hindsight, indicates he knew about Rhaegar's remarriage. When Elia's death comes up in A Storm of Swords, Tywin says he only ordered the Targaryen children killed, to prove the family's loyalty to Robert Baratheon. (Considering Tywin was Mad King Aerys' Hand until the end, this was a necessity.) He "did not think of Elia at all....she was nothing."
In the novels, this comes in the same chapter as a discussion of how important it is to deal with Robb's wife (who in the books survives the Red Wedding). She's a necessary end to tie up, so no one can claim a future baby is Robb Stark's and restart the war. One would think Elia would have needed to be dealt with in the same fashion in the wake of Rhaegar's death.
Tywin declaring Elia unimportant is evidence he knew she wasn't Rhaegar's wife. Moreover, if Tywin didn't need her to prove his loyalty to the new king, that indicates Robert Baratheon also knew.
If they both knew, there's no way the Master of Whispers didn't know.
Fans have always assumed Ned kept Lyanna's secret out of honor. If Robert, Tywin, and Varys knew, this puts an extra spin on it. He couldn't even risk whispering to Cat in the dead of night in their bed. His magically "having a bastard" was suspect enough, and Varys' little birds were everywhere.
It will be interesting to see how Varys reacts when he learns Jon Snow is Aegon Targaryen. Fans will find out how secret Rhaegar's annulment was when Game of Thrones returns on April 14.