How do I file a legal complaint against the MBTA police in Boston for agreeing to help me with an assault case and then don't follow through?

If you're talking about a complaint within the MBTA police department, so that the people involved get reprimanded or whatever, go back to the headquarters, and tell them why you're there.  Someone, however reluctantly, will give you the necesssary forms.

If you're talking about a lawsuit in court, for damages, you can probably forget about it.  In most places, you simply can't sue the police for not doing enough to solve a crime, if for no other reason than that allowing that sort of case could lead to a flood of them, clogging the court, and police officers solving the crimes based on who they were afraid would sue them, rather than genuine law enforcement priorities.  Even in the best of times, most police departments don't have the resources to investigate everything to the last detail.

As unprofessional as the police's conduct was, there is, unfortunately, no lawsuit or legal claim you can place for their failing to follow up.

However, you may certainly file a complaint about this behavior with the police department. You could either go to the precint house where these officer's were based, or you could go to police headquarters; in either event, someone should be able to take your information and complaint and/or give you the proper forms.

If you know your local elected representative (e.g. councilman or woman), you might also try complaining to their office and seeing if they, as your representative, cannot  bring the issue to the police on your behalf.