First of all, how cool was it to see John Noble and Peter Weller hobnobbing on screen together? Just two old scientists exchanging time travel theories and comparing notes on saving/stealing loved ones.
It was the perfect vehicle to build on Walter's struggle about whether to tell Peter or not. In a sense, he'd already been through what Alistair was contemplating. Yes, Walter had crossed to another universe while Alistair was trying to jump back in time, but the result was the same -- be with the person you'd lost. Anyone who's lost a loved one can relate. There's nothing you wouldn't do to be with that person again, even if it means jeopardizing others in the process.
The story also served to further explain the casualties involved in such an event. Wherever Alistair "landed," those people would die, as they did on the subway. He just needed Walter's help to get him back to the exact spot and time to save his fiance. He needed to get back to the field with the hot air balloon.
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