Carl joined Morecambe in the Summer of 2007 in a deal that saw him become the Shrimps record signing.
The attacking midfielder had been a long time target for McIlroy after impressing for the Sandgrounders during the 2006/2007 season, scoring 12 goals from midfield.
Speaking about the signing McIlroy said: "Baker is an exciting player who will be a real addition to our squad.
"He is a terrific player who has great feet and vision and can play in several positions and I am delighted to have secured his services.''
Baker himself said: "I am delighted to have sorted everything out and am now able to concentrate on my football.
"I did have a few clubs interested in signing me but I have known Sammy McIlroy for a while and he is someone I really admire. I always really wanted to sign for him after he spoke to me. I did want League football as well and I was delighted to see Morecambe get promoted I am glad to be here at an exciting time for the club.'
"I always believe I can score a few goals from midfield but also believe I have the capability to make a few goals as well. I love running at defenders and hope I can cause them a few problems this season.''