Publishing in Nature

I am a 5th year PhD student who just submitted my thesis. I wrapped up all my work (or so I thought) and submitted my one manuscript describing a majority of my PhD work a few months ago to Nature Microbiology. The editor rejected it citing lack of scope and interest to broad readership. We filed an appeal and to our surprise (maybe the editor payed a closer attention to the manuscript) the editor agreed to send it for peer review. After a few months, we heard back from the Editor saying the manuscript is rejected once again as central hypothesis are not well supported and there is no significant advance. Going through the three reviewer comments (which were rather lengthy), all three of them agreed that the manuscript deals with an important topic and does extensive work. However all three reviewers had concerns with a few of our central claims and they agree that the central claims are well established through indirect evidence but one or two key experiments could strengthen the claims (I think the central claims are well supported with the insane number of ways we characterised). Apart from this, each of the reviewer had a few experiments they would like us to do. One reviewer says most of the data is expected and is therefore not novel when we give experimental evidence to long standing hypotheses.

Now my PI wants to fight once again and file an appeal and is promising the editor we will do all the experiments in 4-6 months. If the editor rejects, my PI wants me to still do all the suggested experiments before we submit to the next journal. The entire process with Nature Microbiology took about 4 months only to end in rejection. My funding runs out this month. I am stuck in this limbo of waiting for the paper to get accepted somewhere good so I can apply for a decent postdoc. Will this ever end?