We live in an unusual star system. Most of the systems in our Galaxy, that we got a look at are binary star systems. The Solar System should have been, too. Anyway here's the short version of my take on it:
Jupiter is the binary partner to our sun that never quite made the leap to fusion. Most likely because the Sun got there first and blew Jupiter's flame out and swung it into the outer reaches; re-aligning planets and moons on the way.
The new orbit grabbed the outer planets and re-aligned them, too.
The Sun continued it's fusion reaction gaining mass (and gravitational power). On Jupiter's way back in the Suns gravity whipped Jupiter into a new orbit, closer in and less elliptical. This may have been the trip that dragged Mercury into it's devastating orbit.
Once again, almost star Jupiter influenced the orbits of the inner planets and began the internal stresses on the new inner planets that started devastating volcanic eruptions. On the it's way to the outer part of our system, the Outer Planets influenced Jupiter as much as it did them and re-aligned Jupiter's orbit again.
One final trip inward, Jupiter's new orbit dragged tons of asteroids from the Ort Cloud to bombard the planets on it's last trip before it's final settling onto it's current orbit.
Now we are up to The Late Heavy Bombardment.
Venus never recovered from the volcanoes. Mercury was baked into the shape it's in now. Mars barely recovered from the volcanoes when the bombardment finished destroying it's atmosphere. Earth got lucky thanks to it's position between Mars and the Sun and only got a near miss from Jupiter's latest swing through the system.
When our Moon final settled it's orbit it helped drag water up through Earth's crust and helped create the ocean world we now enjoy.