app.js

var Sequelize = require('sequelize');
var DataTypes = Sequelize;

sequelize = new Sequelize('mysql://root@localhost/29165644', {});

var Module = sequelize.define('module', {
    id: DataTypes.INTEGER,
    name: DataTypes.STRING,
    description: DataTypes.STRING,
    category_id: DataTypes.STRING,
    module_type_id: DataTypes.STRING,
    gives_score: DataTypes.INTEGER,
    duration: DataTypes.STRING,
    price: DataTypes.STRING
}, {
    freezeTableName: true
});


Competence = sequelize.define('competence', {
    id: DataTypes.INTEGER,
    name: DataTypes.STRING,
    organization_id: DataTypes.INTEGER,
    competence_type_id: DataTypes.INTEGER
}, {
    freezeTableName:true
})

Module_has_competence = sequelize.define('module_has_competence', {
    id: DataTypes.INTEGER,
    module_id: DataTypes.INTEGER,
    competence_id: DataTypes.INTEGER,
    score: DataTypes.STRING
},{
    freezeTableName: true
})

// Module.hasMany(Competence, {
//     through: 'Module_has_competence',
//     as: {
//         singular: 'competence',
//         plural: 'competence'
//     }
// })

Competence.belongsToMany(Module, {
    through: Module_has_competence,
    as: 'module',
    foreignKey: 'module_id'
})
Module.belongsToMany(Competence, {
    through: Module_has_competence,
    as: 'competence',
    foreignKey: 'competence_id'
})
// Module.hasMany(Competence, {through: Module_has_competence});

Module.find({
    include: [{
        all: true
    }],
    where: {
        id: 1
    }
})
.then(function(data) {
    console.log(data)
})
.catch(function(err) {
    console.trace(err);
});

dump.sql

# ************************************************************
# Sequel Pro SQL dump
# Version 4096
#
# http://www.sequelpro.com/
# http://code.google.com/p/sequel-pro/
#
# Host: 127.0.0.1 (MySQL 5.6.22)
# Database: 29165644
# Generation Time: 2015-03-26 19:08:39 +0000
# ************************************************************


/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
/*!40101 SET NAMES utf8 */;
/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */;
/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */;
/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;


# Dump of table competence
# ------------------------------------------------------------

CREATE TABLE `competence` (
  `id` int(11) unsigned NOT NULL AUTO_INCREMENT,
  `name` varchar(255) DEFAULT NULL,
  `organization_id` int(11) DEFAULT NULL,
  `competence_type_id` int(11) DEFAULT NULL,
  `createdAt` int(11) DEFAULT NULL,
  `updatedAt` int(11) DEFAULT NULL,
  PRIMARY KEY (`id`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;



# Dump of table module
# ------------------------------------------------------------

CREATE TABLE `module` (
  `id` int(11) unsigned NOT NULL AUTO_INCREMENT,
  `name` varchar(255) DEFAULT NULL,
  `description` varchar(255) DEFAULT NULL,
  `category_id` varchar(255) DEFAULT NULL,
  `module_type_id` varchar(255) DEFAULT NULL,
  `gives_score` int(11) DEFAULT NULL,
  `duration` varchar(255) DEFAULT NULL,
  `price` varchar(255) DEFAULT NULL,
  `createdAt` int(11) DEFAULT NULL,
  `updatedAt` int(11) DEFAULT NULL,
  PRIMARY KEY (`id`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;



# Dump of table module_has_competence
# ------------------------------------------------------------

CREATE TABLE `module_has_competence` (
  `id` int(11) unsigned NOT NULL AUTO_INCREMENT,
  `module_id` int(11) DEFAULT NULL,
  `competence_id` int(11) DEFAULT NULL,
  `score` varchar(255) DEFAULT NULL,
  `createdAt` int(11) DEFAULT NULL,
  `updatedAt` int(11) DEFAULT NULL,
  PRIMARY KEY (`id`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;




/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */;
/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;

package.json

{
  "name": "29165644",
  "version": "1.0.0",
  "description": "",
  "main": "index.js",
  "scripts": {
    "test": "echo \"Error: no test specified\" && exit 1"
  },
  "author": "",
  "license": "ISC",
  "dependencies": {
    "mysql": "^2.6.0",
    "sequelize": "^2.0.5",
    "sequelize-mysql": "^1.7.0"
  }
}