"on time" - there is an expected time. We are meeting friends for dinner at 7. I hope we will be on time and we don't make them wait for us.
"in time" - there is a deadline. If we are past this deadline, we will miss the chance to do something. The show starts at 8 p.m. and no one is admitted after the show starts. I hope we will make it to the theater in time.
(Your sample sentences are a little odd. Sometimes we say people or things come "in" -- either to arrive or to finish something. This project has no hope of coming in on time.)