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There are methodologies like Scrum out there but should you go for something more bespoke?

Most organisations impose a hierarchy and expect leaders to lead - so how would a self organising team work?

Most organisations require weekly timesheets, so should you fit in with the organisational cadence. Most individuals work to a weekly cadence too - so why fight what seems natural by imposing a different sized sprint. I have started holding planning meetings on Monday and then review / reflectives on Friday. No daily scrums in-between. I also reserve the right to redirect the team if urgent priorities arise - regardless of what was planned.

Also large organisations are not easy to change to fit the Agile paradigm. They frequently force you down a waterfall approach with gated reviews like requirements review, preliminary and critical design reviews and test readiness reviews.

Organisational issues aside, if working on safety critical software then standards like DO178C and IEC61508 can impose work flows which are far from Agile in nature.

Don't get me wrong there is a place for Agile practices. Software Engineers and leads should understand Agile methodologies and workflow, they should also understand waterfall. A good lead should be able to adapt these to the needs of his team. Too often Agile evangelists can impose as rigid a structure and way of working as Waterfall.

Finally while working software is the ultimate goal, however the importance of documentation cannot be overstated - it reduces dependence on individuals. You need docs for:

Plans on config control, quality, verification, requirements and change management.

Requirements, design, build procedures, software loading procedures, test specs, test reports, release notes, software user guides.