While your son Mitchell returning in 2071 to callously arrest Jill (your wife and his mother) for heresy is horrible enough, you can interact with Jill for a brief window before this happens. If you do, it is revealed that she is too depressed to speak, and despite being an artist, no longer paints or draws anything. This suggests that Jill has alreadybeen broken by a Despair Event Horizon, probably from when Mitchell first abandoned your family or from how terrible life has become by 2071 — or both.
After the Plan is defeated, the victory epilogue has you entering a 2091 simulation of a New Plan that has carried humanity to the stars. In this bright future, your son Mitchell becomes a scientist instead of a religious fanatic who coldly executes his own mother for heresy, and he gathers his own clan (your grandchildren and great-grandchildren) to wish you and your wife a fond farewell as the two of you board humanity's first generation ship to explore interstellar space. While this is played as a happy ending — and after the hell of the earlier simulations, you have more than earned it — you could be forgiven for wondering "Wait, Perry knows this is just another simulation. Doesn't he care that neither his family nor anything he will discover in 'outer space' are real? And speaking of real, back in the real world of 2031, is Dr. Perelman's department really going to keep footing the server bills so that Perry, humanity's first ever AI, can just daydream forever?"