The team is hired by MI6, but things aren't what they seem. As soon as the team breaks into the UN with MI6 agent Ian Gleason, they learn that the mission is to assassinate Jonas, an arms dealer. MI6 blackmails Team Scorpion. They can either help or footage of them breaking into the UN will be released and the team will be tried in international court.
Things only get worse from there. Gleason's hit goes wrong, and he's killed and then incinerated. You would think that this would be the end of the mission, but it's not. Walter wants to kill Jonas because he's a bad guy. This involves Ray translating Polish for Toby, and Toby dragging out the speech of the Polish delegate. Paige poses as a makeup artist with Happy as her assistant. All of this is to get a salami bomb into Jonas' briefcase.
Walter got a court order declaring Megan unfit to make her own decisions regarding her care. He intubated her against her will, and Megan begged Sylvester to never let that happen again.
But wait, there's a twist! Gleason isn't dead. It was all a rouse in order to get Jones for murder. Gleason even cut off a finger to sell it. The reason for the rouse? Olivia Cromwell, Gleason's MI6 buddy, is actually in bed with Jonas. This was done to take both her and Jonas done.