They've been through a lot together. Everything from daily battles to zombie 'pharmacists.' They've worked with and against each other. What started out as an ordinary animosity grew into a powerful friendship. Eventually, that friendship evolved into an even more powerful relationship. Of course, no one could find out, but they didn't mind. They thought that a secret relationship would be more exciting. One of them was familiar with keeping secrets, anyway.
No matter what they went through, Heinz Doofenshmirtz and Perry the Platypus could always find peace in one another's presence.