I kind don't understand what happened. I don't claim it's a plot hole, maybe it's me who didn't get it.

What I understood on the main plot is that over the years Leigh managed to discover the secret Opus Dei group and who were the current 4 priory members, but he was unable to find where the cryptex was and who were the bloodline family. His intention was to find out the family and the sarcophagus and then expose them, so that the world would know the truth and the dark con.

Unable to find this main targets, and seeing that Opus Dei members were slothing, he decided to contact them and expose the priory members, so that they'd get hunt and be forced to move, maybe reach the cryptex, so he'd discover its location.

Ok, he got priory members killed, and on a big luck he got the surviving ppl to contact precisely him to get help to find the secret, and that made him join the quest he wanted to provoke. Silas found them and got captured and the quest begun.

But then, why would the butler release Silas and point the gun to Robert? If Robert and Leigh had the cryptex and were working together on the quest, then Opus Dei's mission was accomplished, and any action they'd do would risk destroying everything. And in fact, Silas stopped their quest and almost got them killed. To not say he knew about the cryptex and could pretty much destroy it.

If Robert hadn't managed to flee, what would Leigh do next? What happens is odd, as Leigh just ignores Robert with the cryptex and stays tied while they deal with Silas, who should be tied and not making trouble to begin with, while shows more interest on killing the butler, who could be of great help to him, and to betray Opus Dei who he had just released. If Aringarosa was out of track and Silas was tied, he should have left them to deal with later and kept focus on working with Robert on the quest, which they were deeply focused on and all that mess just disturbed.

I also don't see any sense on Leigh then showing up to Robert and threatening him to decipher the cryptex.

Again, before Silas was released, Robert was alrdy focusing on it, so there was no need for threats. It'd be both more effective and also safer for Leigh to work together with Robert as friends and have the butler helping and keeping Opus Dei out. By them succeeding, Leigh would know all he needed and have all their support for exposing everything.