Jake fights for the Fusion fuel project, even though no one else believes in it and the lead scientist seems incapable of any fundraising and puts all the pressure onto this young guy. Having joined Josh Brolin's team due to being noticed favorably for insider trading against that firm (and it's easy all you need is an instant message system that sends out 1000 messages, anonymously somehow, to all the big traders in less than a second), he sells his fusion idea to the Chinese -- but Brolin pushes a short-term solar project instead to keep his oil pipelines around for a little longer.
Angry about his boss making the final decision (and a decision to benefit the company and its shareholders - a terrible thing, how can he live with himself?), Jake quits/is fired and goes to Gekko for help.
Gekko tells Jake about a Swiss trust fund he opened for his daughter that will now have $100million in the account - as luck would have it, the exact same figure the fusion project needs to keep on going. Gekko tells Jake to get Winnie to transfer it over to him, and then he'll take the risk to launder the money into the US.
You'll see this one coming a mile away too. So, the money is transferred to Gekko - but the Fusion project is still penniless ... and Gekko disappears to London to start over again.
Gekko uses the $100million to turn it into $1.1billion and is a player again. Jake tracks him down and shows him a video of his unborn grandson and tells him to do the right thing.
The banks are in chaos as the DowJones slumps, and are bailed out by the Government. Meanwhile after an anonymous tip by Jake, Josh Brolin's accounts are investigated and he is brought to justice for insider trading as he profited from the downfall of Jake's mentor's investment bank.
Jake tries to be nice to Winnie, but not very successfully. Gekko shows up, says he deposited a cheque for $100 million to the Fusion project, and wants to be a family again. I guess it's one of those double irony endings, so Gekko still has $1billion, Jake has nothing, the Fusion guys are ready to waste another $100million, Jake's mother's business has collapsed and so she's back as a nurse and the old guy who looks like Yoda does a deal with Gekko to keep his firm afloat.
In the credits we see a birthday party for the little baby with Jake and Winnie back together, and all the family smiling and ready to live happily ever after - although probably watching Gordon closely if he hangs around the pile of birthday presents for too long.