On Scorpion Season 2 Episode 17, Toby lets the Quintis secret slip out during his therapy session with Walter. Sock puppets will get you into trouble, Toby!
Walter's upset, and instead of waiting for the secret to come out, Toby stands on a box and makes the Quintis announcement. Walter's reaction is to bench Toby for the mission. Paige stays behind to try to calm Toby down.
The mission is stopping drones from delivering deadly heroin. The plan was to test out a weapon during a drone test run, but turns out it wasn't so much a test run as a full shipment.
Team Scorpion ends up on the run from the drug runners. Their van gets shot and is now undriveable and Sanchez, the agent who brought them the case, has been shot. Toby talks Happy and Sylvester through stabilizing Sanchez while Walter and Cabe tackle the drug runners.
In the end, everything turns out okay, but Walter still demands that either Quintis breaks up or one of them leaves the team. Paige tries to convince Walter that Toby and Happy work better together now that they are a couple, and that Scorpion needs to evolve. Walter agrees to let Happy and Toby stay Quintis and stay with Scorpion.