...as it must be hard to destroy the bond between a boy and his Doomsday device, however Peter might try to, there's no use to that and yet you can't destroy the bond between a boy and his father and the construction and deconstruction of said bond that takes places tonight.
Oddly how, after experimenting on his son for so long, it's Walter the first to object to other scientists experimenting on Peter, much like Broyles would object to any agent other than Astrid working on his findings, most of them being about Alt-Olivia's relationship with Peter than anything useful to stop the Doomsday machine.
The Machine, however, does say something to Peter or, at least, has that effect as it "programs" him into killing shapeshifters posing as several people within Massive Dynamic and other organizations, Peter doesn't know what he's doing but he must know it's something wrong for he hid it from his family as well as from himself. By the time he takes down the last "mark", Walter has admitted defeat, his son is a living weapon and there's nothing he can do about it.
Be that as it may, either a boy or a weapon, it must be hard being its father.