Dexter frequently uses his boat to dispose of his victims (which could implicate him in The Bay Harbor Butcher murders), and in Season 2, he eventually gets caught doing so, first by wiping his boat clean in front of recently installed security cameras, which he has to hastily remove the files from (Dex, Lies and Videotape) and a second, much worse time when Sergeant James Doakes attaches a GPS Tracking Device onto his boat and follows him to a kill site, where he confronts Dexter and discovers his secret (Resistance is Futile).He also tends to use the boat as a means to bond with people, such as getting back on Rita's good terms by taking her and the kids on a fishing trip at the end of Season 2 (Left Turn Ahead). He also goes fishing with Miguel Prado in the middle of Season 3 and takes Debra, Rita and the kids on a trip in the middle of Season 4. He continues to use the boat throughout Season 4, 5, 6, and even 8, such as when he went out to dispose of A.J. Yates while bonding with his sister and Evelyn Vogel.
In Season 7, Maria LaGuerta discovers a discarded blood slide in the scorched church where Travis Marshall was killed, and compares it to the slides taken by The Bay Harbor Butcher. She sees the similarities between the two, and so decides to clear James Doakes's name (who was believed be The Butcher, though, in reality, was framed by Dexter). LaGuerta works the case independently, even enlisting the help of Thomas Matthews, who thinks that she is nuts and refuses to help her. However, after finding a boat in Doakes's possession and murder weapons with Doakes's fingerprints on them, she suspects that this evidence was planted. She manages to gather a list of boat-owners in Miami, and through process of elimination, narrows it down to Dexter. She arrests and interrogates Dexter, who denies all of the above, and with the intervention of Debra Morgan, LaGuerta is viewed as a demented person. However, when LaGuerta goes too far, Dexter sedates her and Debra shoots her in the chest to protect her brother. However, this leaves Debra guilt-ridden for months.
Louis Greene makes an attempt to sink The Slice of Life. Isaak Sirko comes across Louis and shoots him in the head, and the latter dies on Dexter's boat. George takes Louis out to sea and dumps his body somewhere in the ocean. Later in the season, it seems that Louis's attempt to sink the Slice of Life was unsuccessful, as Dexter is seen with it in the ocean. Furthermore, Dexter discovered Louis' death and proceeded to clean the boat (showing that he cares about the boat's cleanliness).
When Dexter and Hannah McKay are planning to move to Argentina, Dexter no longer feels an urge to kill and so desires to sell his boat to a random person. However, due to some delays (i.e. going after and killing Oliver Saxon), Dexter manages to use the boat one last time for disposing of his sister (who Dexter had to mercy-kill to prevent her from succumbing to her gunshot wound). The boat is then obliterated in Hurricane Laura, when Dexter drives it into the storm upon realizing that he isn't fit to be a father, and needs to live a distant life where he can do no harm. After the storm clears out, the boat's wreckage is found about a mile off-shore, with no apparent survivors. In reality, Dexter had used the emergency life raft  to escape death from the hurricane, and moved on to become a lumberjack in an undisclosed location.
Dexter reveals a lot of information about the boat in Monkey In a Box when attempting to sell it off to a potential Boat Buyer:
''She's a 2001 Century 2901 center console. I had this custom rail put in. New paint. Has a radar, GPS, fish-finder, autopilot, emergency life raft. And I had these twin Yamaha 250 four stroke motors put in. They got just over 400 hours, and when you open them up and you're out there...There's nothing like it.