Hmm, in case you didn't notice the Entity was DYING in the Lavos Timeline. The 400 year reunion hints towards it. Let's see if I can give you guys a qoute of what they say... Ah, here.
Robo: After 400 years of experience, I have come to think that Lavos may not
be responsible for the Gates.
Marle: What do you mean?
Robo: I have come to think that someone, or something wanted us to see all
this. The different events over time, that we have witnessed. It is almost
as if some entity wanted to relive its past.
Ayla: Ayla know! When people die, elders say, see whole life pass by!
Frog: 'Tis true that mortals do relive their most profound memories before
death claimeth them. Yet those memories most often are sad ones.
Robo: Thinking things like "If only I had done this," or "I shouldn't have
done that..." triggers unpleasant, old memories.
Marle: Will that happen when our time comes?
Lucca: Probably... who knows?
Marle: Is there a point in time you'd want to return to, Lucca?
Lucca: No... not really...
Marle: I'm sorry, was that something I shouldn't have asked?
Lucca: It's ok, it's just something I don't like to think about too much.
Frog: Lavos playeth an integral role in the fortunes of this Entity...
Magus: So who is this Entity?
Robo: It is unknown, whose memories these are. It may be something beyond our
comprehension. Our journey may come to an end when we finally discover the
identify of the Entity. Shall we turn in for the night?
They constantly discuss about seeing your whole life pass by. The entity just needs to focus on a certain memory... And viola, we have a Gate!