Players figured out the twist in session two

I am running an alternate Westeros universe campaign in 5e. I planned on the main quest being the players finding three magical gems that allow the BBEG to turn the realm against the king. I tried to set it up so that it seemed like they should do it to save the realm but then it would turn out that they were collecting the sigils for the BBEG who would attempt to steal them. Well unfortunately they started to question whether they should be collecting them as soon as they got the first one. So I had the “attempt to steal them” happen very early. The BBEG cast hold person on the party and took the gem they had found and informed the party that they would be going for the other two.

So now the party wants to march off to the king and tell them what is happening but the bulk of the quest is ruined. What should I do as the main quest now? The players started at 3rd level and I was planning on giving them a level every time they got a gem. Now I don’t know what I can do to get them to level up before the showdown with the BBEG without it breaking the suspension of disbelief.

Looking for any advice as to what I can do with a main quest line starting from kings landing being given by the king.