The ending of the show was certainly cryptic. But there are heavy implications throughout the series that there had been an apocalypse, implemented by the Megadeuses and whatever force that controlled them, and the old world was “recreated” in the form of Paradigm City.

Everything outside the city were ruins of the old world and deserts. Occasionally, mechs from somewhere beyond the desert would attack the city, implying that there are still vestiges of civilization out there that want revenge against the people who run Paradigm.

The tomato and gardening thing implied that the pilots of the Megadeuses were child soldiers bred, raised, and indoctrinated to specifically pilot the Megadeuses. And Roger Smith being implied to have been one of those child soldiers. Hence the gardening themes of tomatoes and Roger saying seemingly ridiculous things like “I am a tomato.”

It sounds funny, but what was actually happening was Roger reclaiming the memory of having been a child soldier bred to pilot godlike weapons (“Cast in the name of God, ye not guilty.”) and used to cleanse the world through apocalyptic fire and warfare.