gistfile1.sh

# showmigrations comes from https://github.com/MarkusH/django/tree/ticket23359-2
$ python manage.py showmigrations --plan -v 2
[X]  contenttypes.0001_initial
[X]  auth.0001_initial ... (contenttypes.0001_initial)
[X]  admin.0001_initial ... (auth.0001_initial, contenttypes.0001_initial)
[X]  auth.0002_alter_permission_name_max_length ... (auth.0001_initial)
[X]  auth.0003_alter_user_email_max_length ... (auth.0002_alter_permission_name_max_length)
[X]  auth.0004_alter_user_username_opts ... (auth.0003_alter_user_email_max_length)
[X]  auth.0005_alter_user_last_login_null ... (auth.0004_alter_user_username_opts)
[X]  sites.0001_initial
[X]  flatpages.0001_initial ... (sites.0001_initial)
[X]  otherapp.0001_initial
[X]  testapp.0001_initial ... (auth.0001_initial, otherapp.0001_initial)
[X]  otherapp.0002_auto_20141127_1753 ... (auth.0001_initial, testapp.0001_initial, otherapp.0001_initial)
[X]  redirects.0001_initial ... (sites.0001_initial)
[X]  sessions.0001_initial

otherapp.migrations.0001_initial.py

# -*- coding: utf-8 -*-
from __future__ import unicode_literals

from django.db import models, migrations


class Migration(migrations.Migration):

    dependencies = [
    ]

    operations = [
        migrations.CreateModel(
            name='ThroughModel',
            fields=[
                ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
            ],
            options=None,
            bases=None,
        ),
    ]

otherapp.migrations.0002_auto_20141127_1746.py

# -*- coding: utf-8 -*-
from __future__ import unicode_literals

from django.db import models, migrations
from django.conf import settings


class Migration(migrations.Migration):

    dependencies = [
        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
        ('testapp', '0001_initial'),
        ('otherapp', '0001_initial'),
    ]

    operations = [
        migrations.AddField(
            model_name='throughmodel',
            name='foo',
            field=models.ForeignKey(to='testapp.Foo'),
            preserve_default=True,
        ),
        migrations.AddField(
            model_name='throughmodel',
            name='user',
            field=models.ForeignKey(to=settings.AUTH_USER_MODEL),
            preserve_default=True,
        ),
    ]

otherapp.models.py

from django.db import models

# Create your models here.

class ThroughModel(models.Model):
    foo = models.ForeignKey('testapp.Foo')
    user = models.ForeignKey('auth.User')

testapp.migrations.0001_initial.py

# -*- coding: utf-8 -*-
from __future__ import unicode_literals

from django.db import models, migrations
from django.conf import settings


class Migration(migrations.Migration):

    dependencies = [
        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
        ('otherapp', '0001_initial'),
    ]

    operations = [
        migrations.CreateModel(
            name='Foo',
            fields=[
                ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
                ('users', models.ManyToManyField(through='otherapp.ThroughModel', to=settings.AUTH_USER_MODEL)),
            ],
            options=None,
            bases=None,
        ),
    ]

testapp.models.py

from django.db import models


class Foo(models.Model):
    users = models.ManyToManyField('auth.User', through='otherapp.ThroughModel')