I’m having a complete DM creative block. Anything to help the juices flow will be greatly appreciated.   

We’ve got to the end of the chain of autumn (fall) events in dragon season and instead of attuning to the stone and going on their merry way to find the treasure the group have ‘done the right thing’ and handed it over ‘Laeral’. Obvs Laeral is actually Jarlaxle in disguise and in what I thought was a great cliffhanger moment he announced ‘and now you will die!’

But... now I don’t know what to do. Surely he would kill the group (which, after reading his stats he will certainly do), get the gold and have his way with Waterdeep? There doesn’t seem to be a link for them to ally with him. Any ideas? 

I've been over the module and I have a few suggestions:

Note: It is assumed that Jarlaxle turns back into his true form before "revealing his plan" and then escaping. Typical villain behavior.

Suggestion A: As they PCs start to fight with Jarlaxle, the true Laeral Silverhand teleports in. She and Jarlaxle have been communicating, as seen in the module, and she would be very disappointed in him. She may shame him and force him to hand over the stone. From there, before the stone is give, Jarlaxle can place a curse on it. Any person who holds the stone who knew what it was, automatically forgets. Jarlaxle asks for it back, but Laeral denies this request and gives it to the party instead since she thinks it is a useless piece of rock. The party can then go from there.

Suggestion B: Debuff Jarlaxle. Jarlaxle is a very powerful villain. In the final, after-the-loot scene, reinforcements are usually necessary to defeat him. Have the players "wound him" to near death and make him hand over the stone to spare him. This may be because he was in a fight previously (describe this to the players), he left his magic items at home, he is ill, or some other reason. This makes the players get cocky and when they fight him outside of the vault, they may find him to be a bit more wily than he was before.

I hope you can use one of these solutions. Happy DMing!

Great suggestions thanks! I appreciate you taking the time. 

Think I may go for a spin on suggestion A. 

Of course! Anything for a fellow DM. Good luck with the campaign. I can't wait to hear how it goes.

Why would he fight the group? He has the thing he wants. I think he would just surreptitiously make his way back to the boats and start finding the treasure. Fighting them would only cause problems for him. Spending resources, possibly revealing himself, what to do with the bodies, possible law enforcement actions, etc.

I'd say there's no harm in a reset to the moment before he transforms as long as your group agrees to it. It'll keep things moving along nicely. 

So I didn't reset and I ended up fighting the characters, but it didn't turn out too badly. Jarlaxle and the 5(!) elite drow warriors were more than a match. The druid bear formed and tried to maul Jarlaxle, which he dodged and the urban ranger shot at him, which he dodged. After two rounds of initiative 3 of the 5 characters were down and the others ran away to get help from the guard. The guard blew their whistles for back up, which Jarlaxle heard and exited stage right with his cronies. He quipped that this wasn't game enough for him and flounced off with the stone. Felt ok and the group were happy with that as they recovered back in Trollskull. 

I needed to buy some time to figure out how they were to find Jarlaxle and the stone again. So I got the group to go on the Zhent side mission to assassinate Skeemo. I've just finished the episode with a naked druid PC in the middle of the Way of Dragons after the assassination attempt failed! 

I'm not familiar with this module, so my advice can only be used generically.

1) Perhaps the characters retrieved and gave the incorrect or fake stone to Jarlaxle without either group realizing it and now both are on the hunt for the correct stone.

2) If the characters had an idea or could research the idea of where the stone was to be used, they could try to head there for, essentially, round 2 against Jarlaxle.