The subject has uncontrolled, significant intercurrent or recent illness including, but not limited to, the following conditions: * Cardiovascular disorders including: ** Congestive heart failure (CHF): New York Heart Association (NYHA) class III (moderate) or class IV (severe) at the time of screening ** Concurrent uncontrolled hypertension defined as sustained BP > 140 mm Hg systolic, or > 90 mm Hg diastolic despite optimal antihypertensive treatment within 7 days of the first dose of study treatment ** Any history of congenital long QT syndrome ** Any of the following within 6 months before the first dose of study treatment: *** Unstable angina pectoris *** Clinically-significant cardiac arrhythmias *** Stroke (including transient ischemic attack [TIA], or other ischemic event) *** Myocardial infarction *** Thromboembolic event requiring therapeutic anticoagulation (note: subjects with a venous filter [e.g. vena cava filter] are not eligible for this study)* Gastrointestinal disorders particularly those associated with a high risk of perforation or fistula formation including: ** Any of the following within 28 days before the first dose of study treatment*** Intra-abdominal tumor/metastases invading GI mucosa *** Active peptic ulcer disease*** Inflammatory bowel disease (including ulcerative colitis and Crohn�s disease), diverticulitis, cholecystitis, symptomatic cholangitis or appendicitis *** Malabsorption syndrome ** Any of the following within 6 months before the first dose of study treatment: *** Abdominal fistula *** Gastrointestinal perforation *** Bowel obstruction or gastric outlet obstruction *** Intra-abdominal abscess; note: complete resolution of an intra-abdominal abscess must be confirmed prior to initiating treatment with cabozantinib even if the abscess occurred more than 6 months before the first dose of study treatment* Other disorders associated with a high risk of fistula formation including percutaneous endoscopic gastrostomy (PEG) tube placement within 3 months before the first dose of study therapy * Other clinically significant disorders such as: ** Serious non-healing wound/ulcer/bone fracture within 28 days before the first dose of study treatment ** History of organ transplant, including allogeneic bone marrow transplant ** Concurrent uncompensated hypothyroidism or thyroid dysfunction within 7 days before the first dose of study treatment ** History of major surgery as follows:*** Major surgery within 3 months of the first dose of cabozantinib if there were no wound healing complications or within 6 months of the first dose of cabozantinib if there were wound complications *** Minor surgery within 1 month of the first dose of cabozantinib if there were no wound healing complications or within 3 months of the first dose of cabozantinib if there were wound complications ** In addition, complete wound healing from prior surgery must be confirmed at least 28 days before the first dose of cabozantinib irrespective of the time from surgery The participant has uncontrolled, significant intercurrent or recent illness including, but not limited to, the following conditions:* Cardiovascular disorders including:** Congestive heart failure (CHF): New York Heart Association (NYHA) class III (moderate) or class IV (severe) at the time of screening** Concurrent uncontrolled hypertension defined as sustained blood pressure (BP) > 140 mmHg systolic, or > 90 mmHg diastolic despite optimal antihypertensive treatment within 7 days of the first dose of study treatment** Any history of congenital long QT syndrome** Any of the following within 6 months before the first dose of study treatment:*** Unstable angina pectoris*** Clinically-significant cardiac arrhythmias*** Stroke (including transient ischemic attack [TIA], or other ischemic event)*** Myocardial infarction*** Thromboembolic event requiring therapeutic anticoagulation (note: participants with a venous filter [e.g. vena cava filter] are not eligible for this study)* Gastrointestinal disorders particularly those associated with a high risk of perforation or fistula formation including:** Any of the following within 28 days before the first dose of study treatment*** Active peptic ulcer disease*** Inflammatory bowel disease (including ulcerative colitis and Crohn�s disease), diverticulitis, cholecystitis, symptomatic cholangitis or appendicitis*** Malabsorption syndrome** Any of the following within 6 months before the first dose of study treatment:*** Abdominal fistula*** Gastrointestinal perforation*** Bowel obstruction or gastric outlet obstruction*** Intra-abdominal abscess; note: complete resolution of an intra-abdominal abscess must be confirmed prior to initiating treatment with cabozantinib even if the abscess occurred more than 6 months before the first dose of study treatment Gastrointestinal disorders particularly those associated with a high risk of perforation or fistula formation including:* Any of the following within 28 days before the first dose of study treatment** Intra-abdominal tumor/metastases invading GI mucosa** Active peptic ulcer disease,** Inflammatory bowel disease (including ulcerative colitis and Crohn�s disease), diverticulitis, cholecystitis, symptomatic cholangitis or appendicitis** Malabsorption syndrome* Any of the following within 6 months before the first dose of study treatment:** Abdominal fistula** Gastrointestinal perforation** Bowel obstruction or gastric outlet obstruction** Intra-abdominal abscess; note: complete resolution of an intra-abdominal abscess must be confirmed prior to initiating treatment with cabozantinib even if the abscess occurred more than 6 months before the first dose of study treatment Patients with any of the following conditions are excluded: serious or non-healing wound, ulcer; history of abdominal fistula, gastrointestinal perforation, or intra-abdominal abscess within 28 days of treatment; coronary/peripheral artery bypass graft or stenting within the past 12 months; or cerebrovascular accident (CVA) or transient ischemic attack within the past 12 months Patients who have had evidence of active or acute diverticulitis, intra-abdominal abscess, gastrointestinal (GI) obstruction and abdominal carcinomatosis which are known risk factors for bowel perforation should be evaluated for the potential need for additional treatment before coming on study History of abdominal fistula, gastrointestinal perforation or intra-abdominal abscess within 28 days or manifestations of malabsorption due to prior gastrointestinal (GI) surgery or GI disease that may alter the absorption of MLN0128 (TAK-228) History of abdominal fistula, gastrointestinal perforation, or intra-abdominal abscess within 6 months prior to day 1 Subjects with any condition that may increase the risk of gastrointestinal bleeding or gastrointestinal perforation, including:* Active peptic ulcer disease* Known intraluminal metastatic lesions* Inflammatory bowel disease (e.g., ulcerative colitis, Crohn�s disease) or other gastrointestinal conditions which increase the risk of perforation* History of abdominal fistula, gastrointestinal perforation or intra-abdominal abscess within 28 days prior to beginning study treatment The subject has uncontrolled, significant intercurrent or recent illness including, but not limited to, the following conditions:* Cardiovascular disorders including:** Congestive heart failure (CHF): New York Heart Association (NYHA) class III (moderate) or class IV (severe) at the time of screening** Concurrent uncontrolled hypertension defined as sustained blood pressure (BP) > 150 mm Hg systolic, or > 90 mm Hg diastolic despite optimal antihypertensive treatment within 7 days of the first dose of study treatment** Any history of congenital long QT syndrome** Any of the following within 6 months before the first dose of study treatment:*** Unstable angina pectoris*** Clinically-significant cardiac arrhythmias*** Stroke (including transient ischemic attack [TIA], or other ischemic event)*** Myocardial infarction*** Thromboembolic event requiring therapeutic anticoagulation (note: subjects with a venous filter [e.g. vena cava filter] are not eligible for this study)* Gastrointestinal disorders particularly those associated with a high risk of perforation or fistula formation including:** Any of the following within 28 days before the first dose of study treatment*** Intra-abdominal tumor/metastases invading GI mucosa*** Any evidence of active peptic ulcer disease, patients must be completely recovered*** Any evidence of inflammatory bowel disease (including ulcerative colitis and Crohn�s disease), diverticulitis, cholecystitis, symptomatic cholangitis or appendicitis, patients must be completely recovered from these conditions*** Malabsorption syndrome** Any of the following within 6 months before the first dose of study treatment:*** Abdominal fistula*** Gastrointestinal perforation*** Bowel obstruction or gastric outlet obstruction*** Intra-abdominal abscess; note: complete resolution of an intra-abdominal abscess must be confirmed prior to initiating treatment with cabozantinib even if the abscess occurred more than 6 months before the first dose of study treatment* Other disorders associated with a high risk of fistula formation including percutaneous endoscopic gastrostomy (PEG) tube placement within 3 months before the first dose of study therapy * Other clinically significant disorders such as:** Active infection requiring systemic treatment within 28 days before the first dose of study treatment** Serious non-healing wound/ulcer/bone fracture within 28 days before the first dose of study treatment** History of organ transplant** Concurrent uncompensated hypothyroidism or thyroid dysfunction within 7 days before the first dose of study treatment** History of major surgery as follows:*** Major surgery within 12 weeks before the first dose of study treatment; complete wound healing from major surgery must have occurred 1 month before the first dose of study treatment*** Minor surgery (including uncomplicated tooth extractions) within 28 days before the first dose of study treatment with complete wound healing at least 10 days before the first dose of study treatment; subjects with clinically relevant ongoing complications from prior surgery are not eligible Patients who have had evidence of active or acute diverticulitis, intra-abdominal abscess, gastrointestinal (GI) obstruction and abdominal carcinomatosis should be evaluated for the potential need for additional treatment before coming on study Gastrointestinal disorders particularly those associated with a high risk of perforation or fistula formation including:* Any of the following that have not resolved within 28 days before the first dose of study treatment** Intra-abdominal tumor/metastases invading GI mucosa** Active peptic ulcer disease, diverticulitis, cholecystitis, symptomatic cholangitis or appendicitis** Malabsorption syndrome* Any of the following within 6 months before the first dose of study treatment:** Abdominal fistula** Gastrointestinal perforation** Bowel obstruction or gastric outlet obstruction** Intra-abdominal abscess; Note: complete resolution of an intra-abdominal abscess must be confirmed prior to initiating treatment with cabozantinib even if the abscess occurred more than 6 months before the first dose of study treatment Patients who have had evidence of active or acute diverticulitis, intra-abdominal abscess, GI obstruction and abdominal carcinomatosis which are known risk factors for bowel perforation should be evaluated for the potential need for additional treatment before coming on study Patients who have had evidence of active or acute diverticulitis, intra-abdominal abscess, gastrointestinal (GI) obstruction, fistula and abdominal carcinomatosis should be evaluated for the potential need for additional treatment before coming on study Any of the following within 2 months of registration: active peptic ulcer disease, diverticulitis, cholecystitis, symptomatic cholangitis or appendicitis, malabsorption syndrome; any of the following within 6 months of registration: intra-abdominal abscess, gastrointestinal obstruction requiring parenteral hydration and/or nutrition, gastrointestinal perforation; Note: complete resolution of an intra-abdominal abscess must be confirmed prior to registration even if the abscess occurred more than 6 months prior to registration Participants who have had evidence of Clostridium (C.) difficile infection, active or acute diverticulitis, intra-abdominal abscess, intra-abdominal abscess, gastrointestinal (GI) obstruction and abdominal carcinomatosis, which are known risk factors for bowel perforation, should be evaluated for the potential need for additional treatment before coming on study History of intra-abdominal abscess within the past 3 months History of intra-abdominal abscess within the past 3 months Patients who have had evidence of active or acute diverticulitis, intra-abdominal abscess, gastrointestinal (GI) obstruction and abdominal carcinomatosis which are known risk factors for bowel perforation should be evaluated for the potential need for additional treatment before coming on study Patients who have a history of fistula, gastrointestinal ulcer or perforation, or intra-abdominal abscess within 3 months of study enrollment are not eligible History of abdominal fistula, intra-abdominal abscess, or gastrointestinal perforation within the 3 months prior to enrollment No history of bowel obstruction, abdominal fistula, gastrointestinal perforation, or intra-abdominal abscess within past 12 months Patients who have had evidence of active or acute diverticulitis, intra-abdominal abscess, gastrointestinal (GI) obstruction and abdominal carcinomatosis which are known risk factors for bowel perforation should be evaluated for the potential need for additional treatment before coming on study History of abdominal/pelvic or tracheoesophageal fistula or gastrointestinal perforation and/or abscess within 6 months prior to initiation of treatment Patients who have had evidence of active or acute diverticulitis, intra-abdominal abscess, gastrointestinal (GI) obstruction and abdominal carcinomatosis which are known risk factors for bowel perforation should be evaluated for the potential need for additional treatment before coming on study History of abdominal/pelvic fistula, gastrointestinal perforation and/or intraabdominal abscess within 6 months prior to day 1 History of abdominal fistula, gastrointestinal perforation or intra-abdominal abscess within 6 months prior to day 1 Participants may not have had a history of intra-abdominal abscess within the past 6 months