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HG Wells has returned to the Warehouse in her full agent status, and Artie isn't hiding his anger about it. The tension is broken, however, with a surprise visit from Rebecca, a Warehouse agent from the 1960s, with a request for Pete and Myka to go back in time and close a case that she and her partner, Jack, were never able to wrap up: An artifact that turns people to glass, and a man who killed three of his secretaries, and his wife, with it. HG determines that Pete and Myka have already done this via a time machine that she invented, where a participant's consciousness can jump into the body of another person for almost a day. Pete's ready to go, but Myka's not convinced until she sees herself - transported back in time, in the person of Rebecca - telling her present self to do it. With Artie in the field, there's no one to tell them no.
Back in 1961, Pete and Myka quickly do some recon on the women and their killer, all the while trying not to alter history. After discovering a secret meeting between the killer, Jonah, and his next victim, Blank, they follow the pair to a secret rendezvous point. But Pete can't watch her die, and tries to warn Blank. Fleeing him, she runs straight into a cloaked figure, who instantly turns her to glass and disappears. Just then, Jonah arrives. He, Pete and Myka are stumped as to what's going on, but Pete and Myka convince Jonah to trust them. He takes them back to his house to warn his wife and see if anything in their home could be responsible for the glassy deaths. Jonah's wife arrives, and, seeing Myka, assumes the worst. A struggle ensues and she stabs Pete with a dagger - and he turns to glass. Myka manages to wrest the dagger from Pete's arm, and he returns to normal, but in the melee, Jonah's wife is stabbed, spelling the end of her life. Pete and Myka warn Jonah that he has to flee to avoid suspicion, and set about making the film that will make the whole encounter possible.
Back in the present day, Artie returns to discover the secret plan, and is furious that anyone trusted HG or her machine. He threatens to shut down the power - which would end Pete and Myka - and it takes the pleas of Claudia, HG and Rebecca together to convince him to let HG continue with the plan. Out of options, Artie relents, and they attempt to supply the time machine with enough power to bring Pete and Myka back from the '60s.
Racing to the Warehouse to put the dagger in safe keeping before they're sent back to 2010, Pete and Myka feel the fluctuations in power, and have no choice but to stop their car at a nearby cherry orchard and bury the dagger near one of the trees. In the present day, with his agents safe, Artie is finally mollified, and decides HG can be trusted, after all. And Rebecca, at the end of her life, makes a final request: To travel back in time to see Jack one more time. At the sight of him as a young man, she kisses him, beginning a lifelong romance - all over again.