How to Associate/tiggger JavaScript with HTM file

Respected Community Members,

                         We recently started playing with CRM 2013 and I got one free navigation plugin from external source. I install that plugin and it does work just fine.

Now I need to customize the solution according to my corporate needs , so I extracted solution which gave me 4 files (1) jQuery file 2) custom JavaScript file 3) htm file 4) css file ). I customized code little bit, and try to create a plugin with those web resources and publish the plugin.

I added that htm file to footer of the Account Page which shows up without issue. But some how my javascript doesn't work which suppose to populate the htm file.

Any idea how to resolve this issue?? How can I make sure whether JavaScript triggers when htm file load?? is there a way to associate them??

Thanks,

Nick