I understand well enough. Maybe you should take another look at my explanation. It can't be that complicated.
Let me give it another shot, though:
1) Annorax is hoping to get his wife back after to hundred years and that means that the ship remains stuck in the same time period otherwise timeline or not, she'd be long dead no matter what he did.
2) Annorax assistant says that for more than a hundred years he's been celebrating the birthdays of the dead and that means that the ship is moving forward in time.
You do get that these two statements are in stark contradiction, don't you?
1) Annorax is not hoping to get his wife back. he is hoping to restore her existence, because in normal space time, she never existed.
2) The ship exists outside normal space time, The passage of time is an artifact of the weapon, and the ship itself.
3) Once Annorax restores his colony and his family not in the present but in existence, THEN
4) he would have spent his life with her
instead of wandering around, outside normal space time trying to restore a colony.
this is the paradox
5) He doesn't realize the only way to gain his objective is to :
a) use the weapon to remove the weapon itself from history. if there was never a weapon, he might have spent his life with his wife
b) remove himself from history. without him, there would be no one to make the weapon and therefore no weapon with which to erase himself, so he would be restored and he might have spent his life with his wife
c) or both.
This is the irony
6) After the weapon restores everything, he is seen back oh his colony, none of this ever happened, and he's designing the weapon.
7) Does he complete the weapon, this starting this all over again? I think so, but maybe his getting up to enjoy the day with his wife makes him decide to never finish. I doubt this, but you can read the ending either way.
Your confusion is that he's trying to "get his wife back" in some sort of present time. You also don't get that were he to achieve restoring his wife in history, he never would have had to restore his wife in history, and wouldn't exist in the present.
You don't understand the paradox.
b) use the weapon to remove himself