On Scorpion Season 4 Episode 13, Team Scorpion's latest case is to inspect Safeco's doomsday bunker, but they are instructed to leave Toby behind. The reasoning becomes clear when Sly, Walter, Happy, and Florence get to the bunker to find Quincy waiting for them.
That's right, Toby's nemesis Quincy who stole his fiancée, Amy. Yeah, it's a little awkward, and it only gets worse when Toby shows up at the bunker anyway and learns that Team Scorpion is working with Quincy and Amy.
To make matters worse, the reason Quincy didn't want Toby at the bunker is because he programed Toby as a threat. As soon as Dorie, the bunker's AI system, spots Toby in the bunker, she initiates lockdown procedures.
Now, Team Scorpion has to try to escape the bunker and outsmart Dorie, who is focusing her attention on eliminating Toby, even if it means killing everyone else in the bunker. The bunker has some kinks to work out.
Before Dorie disables all communications, Walter is able to get a message to Paige. She and Cabe manage to get through to the bunker's designer, and he informs them that he built a secret entrance.
Team Scorpion is able to save the day and get out of the bunker, no thanks to Quincy and his cowardice. Happy is able to bond with Amy, and Walter manages to make matters worse after spilling the "married to Florence" dream news to Florence and Paige.